Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xbg Working: n-9-19.cluster.ucsf.bkslab.org:/scratch/xiaobo/318708/xbg-8058115.33 Result: /scratch/xiaobo/318708/xbg-8058115.33 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbg Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xbg mkdir: created directory `/scratch/xiaobo/318708' mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33' /scratch/xiaobo/318708/xbg-8058115.33 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working' mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/protonate' Storing results in /scratch/xiaobo/318708/xbg-8058115.33/finished Working in /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 /scratch/xiaobo/318708/xbg-8058115.33/working/protonate /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Using inputs as protomers/tautomers. No processing done 474 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/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Bulk generating 3D conformations all protomers in /scratch/xiaobo/318708/xbg-8058115.33/working/3D mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/318708/xbg-8058115.33/working/protonate/xbg-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 ZINC000347489742 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building' mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347489742 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/1 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347489742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347489742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347489742 none Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 47, 47, 26, 47, 47, 24, 24, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 24, 24, 24, 47, 47, 36, 47, 47, 24, 24, 24, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/2 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347489742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347489742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347489742 none Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 46, 46, 33, 46, 46, 24, 24, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 46, 46, 36, 46, 46, 24, 24, 24, 6, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347489742 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/finished' Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 Building ZINC000347489742 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347489742 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 1) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347489742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347489742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347489742 none Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 47, 47, 26, 47, 47, 24, 24, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 24, 24, 24, 47, 47, 36, 47, 47, 24, 24, 24, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 2) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347489742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347489742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347489742 none Cc1nn(c2ccccc2)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 46, 46, 33, 46, 46, 24, 24, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 46, 46, 36, 46, 46, 24, 24, 24, 6, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347489742 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347489742 Building ZINC000347502382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347502382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/3 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347502382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347502382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347502382 none Cc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 49, 19, 19, 19, 19, 19, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 49, 49, 19, 19, 10, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/4 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347502382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347502382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347502382 none Cc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 19, 19, 19, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 49, 49, 19, 19, 10, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347502382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 Building ZINC000347502382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347502382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 3) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347502382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347502382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347502382 none Cc1ccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 49, 19, 19, 19, 19, 19, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 49, 49, 19, 19, 10, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 4) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347502382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347502382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347502382 none Cc1ccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 19, 19, 19, 10, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 49, 49, 19, 19, 10, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347502382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347502382 Building ZINC000347504667 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347504667 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/5 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2) `ZINC000347504667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347504667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504667 none CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 16, 23, 23, 23, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 4, 3, 3, 3, 3, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/6 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2) `ZINC000347504667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347504667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504667 none CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 16, 24, 24, 24, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 4, 3, 3, 3, 3, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347504667 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 Building ZINC000347504667 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347504667 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 5) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2) `ZINC000347504667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347504667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504667 none CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 16, 23, 23, 23, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 4, 3, 3, 3, 3, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 6) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2) `ZINC000347504667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347504667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504667 none CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 16, 24, 24, 24, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 4, 3, 3, 3, 3, 24, 24, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347504667 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504667 Building ZINC000347504671 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347504671 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/7 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2) `ZINC000347504671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347504671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504671 none CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 16, 25, 25, 25, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 4, 3, 3, 3, 3, 25, 25, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/8 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2) `ZINC000347504671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347504671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504671 none CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 16, 23, 23, 23, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 4, 3, 3, 3, 3, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347504671 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 Building ZINC000347504671 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347504671 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 7) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2) `ZINC000347504671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347504671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504671 none CCOc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 16, 25, 25, 25, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 4, 3, 3, 3, 3, 25, 25, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 8) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2) `ZINC000347504671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347504671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347504671 none CCOc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)O[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 16, 23, 23, 23, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 4, 3, 3, 3, 3, 23, 23, 23, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347504671 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504671 Building ZINC000347504801 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347504801 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/9 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347504801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347504801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347504801 none CCCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 49, 49, 49, 49, 49, 25, 25, 13, 13, 13, 13, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/10 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347504801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347504801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347504801 none CCCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 25, 25, 13, 13, 13, 13, 6, 5, 5, 5, 5] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347504801 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 Building ZINC000347504801 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347504801 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 9) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347504801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347504801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347504801 none CCCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 2, 5, 5, 49, 49, 49, 49, 49, 25, 25, 13, 13, 13, 13, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 10) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347504801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347504801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347504801 none CCCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 25, 25, 13, 13, 13, 13, 6, 5, 5, 5, 5] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/318708/xbg-8058115.33/working/building/ZINC000347504801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347504801 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347504801 Building ZINC000347505382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347505382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/11 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347505382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347505382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347505382 none O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 12, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 32, 44, 44, 43, 32, 43, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/12 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347505382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347505382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347505382 none O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 12, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 32, 44, 44, 43, 32, 43, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347505382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 Building ZINC000347505382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347505382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 11) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347505382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347505382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347505382 none O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 12, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 32, 44, 44, 43, 32, 43, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 12) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347505382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347505382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347505382 none O=C(Nc1cc2c(cc1Cl)OCCCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 16, 12, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 32, 44, 44, 43, 32, 43, 44, 44, 44, 44, 44, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 44, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347505382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347505382 Building ZINC000347508092 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347508092 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/13 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000347508092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347508092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347508092 none COc1cccc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 20, 20, 20, 20, 20, 20, 20, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 37, 37, 37, 20, 20, 20, 12, 6, 6, 6, 6] 46 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/14 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000347508092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347508092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347508092 none COc1cccc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 20, 20, 20, 20, 20, 20, 20, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 37, 37, 37, 20, 20, 20, 12, 6, 6, 6, 6] 46 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347508092 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 Building ZINC000347508092 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347508092 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 13) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000347508092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347508092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347508092 none COc1cccc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 20, 20, 20, 20, 20, 20, 20, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 37, 37, 37, 20, 20, 20, 12, 6, 6, 6, 6] 46 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 14) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21) `ZINC000347508092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347508092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347508092 none COc1cccc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 20, 20, 20, 20, 20, 20, 20, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 20, 20, 37, 37, 37, 20, 20, 20, 12, 6, 6, 6, 6] 46 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347508092 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508092 Building ZINC000347508233 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347508233 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/15 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(CC)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347508233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347508233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347508233 none CCOC(=O)c1cc(CC)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [32, 24, 22, 8, 22, 8, 8, 8, 8, 20, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 32, 8, 20, 20, 20, 20, 20, 4, 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, 37, 38, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/16 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(CC)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347508233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347508233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347508233 none CCOC(=O)c1cc(CC)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [32, 24, 22, 8, 22, 8, 8, 8, 8, 20, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 32, 8, 20, 20, 20, 20, 20, 4, 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, 37, 38, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347508233 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 Building ZINC000347508233 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347508233 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 15) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1cc(CC)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347508233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347508233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347508233 none CCOC(=O)c1cc(CC)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [32, 24, 22, 8, 22, 8, 8, 8, 8, 20, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 32, 8, 20, 20, 20, 20, 20, 4, 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, 37, 38, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 16) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1cc(CC)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347508233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347508233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347508233 none CCOC(=O)c1cc(CC)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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: [32, 24, 22, 8, 22, 8, 8, 8, 8, 20, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 32, 32, 8, 20, 20, 20, 20, 20, 4, 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, 37, 38, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347508233 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347508233 Building ZINC000347510021 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347510021 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/17 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347510021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347510021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347510021 none COC(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 18, 50, 18, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 50, 50, 50, 18, 18, 5, 4, 4, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/18 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347510021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347510021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347510021 none COC(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 18, 50, 18, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 50, 50, 50, 18, 18, 5, 4, 4, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347510021 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 Building ZINC000347510021 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347510021 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 17) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347510021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347510021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347510021 none COC(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 18, 50, 18, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 50, 50, 50, 18, 18, 5, 4, 4, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 18) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347510021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347510021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347510021 none COC(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 18, 50, 18, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 50, 50, 50, 18, 18, 5, 4, 4, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347510021 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510021 Building ZINC000347510157 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347510157 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/19 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl) `ZINC000347510157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347510157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347510157 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [38, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 39, 25, 25, 25, 38, 38, 38, 25, 6, 5, 5, 5, 5, 39, 39, 39, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/20 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl) `ZINC000347510157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347510157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347510157 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [38, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 39, 25, 25, 25, 38, 38, 38, 25, 6, 5, 5, 5, 5, 39, 39, 39, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347510157 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 Building ZINC000347510157 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347510157 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 19) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl) `ZINC000347510157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347510157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347510157 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [38, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 39, 25, 25, 25, 38, 38, 38, 25, 6, 5, 5, 5, 5, 39, 39, 39, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 20) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl) `ZINC000347510157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347510157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347510157 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OC)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [38, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 39, 25, 25, 25, 38, 38, 38, 25, 6, 5, 5, 5, 5, 39, 39, 39, 25] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347510157 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347510157 Building ZINC000347520315 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347520315 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/21 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347520315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347520315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347520315 none COC(=O)c1c(C)c(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 50, 24, 24, 24, 24, 24, 24, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 50, 50, 50, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/22 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)c(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347520315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347520315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347520315 none COC(=O)c1c(C)c(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 23, 50, 23, 23, 23, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 23, 23, 23, 23, 23, 23, 6, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347520315 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 Building ZINC000347520315 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347520315 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 21) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1c(C)c(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347520315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347520315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347520315 none COC(=O)c1c(C)c(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 50, 24, 24, 24, 24, 24, 24, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 50, 50, 50, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 22) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1c(C)c(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347520315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347520315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347520315 none COC(=O)c1c(C)c(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 23, 50, 23, 23, 23, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 23, 23, 23, 23, 23, 23, 6, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347520315 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347520315 Building ZINC000347538241 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347538241 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/23 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(C)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347538241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347538241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347538241 none CCOC(=O)c1c(C)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 12, 45, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/24 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(C)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347538241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347538241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347538241 none CCOC(=O)c1c(C)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 12, 45, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347538241 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 Building ZINC000347538241 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347538241 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 23) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1c(C)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347538241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347538241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347538241 none CCOC(=O)c1c(C)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 12, 45, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 24) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1c(C)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347538241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347538241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347538241 none CCOC(=O)c1c(C)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 12, 45, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347538241 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347538241 Building ZINC000347524608 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347524608 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/25 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347524608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524608 none O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 45, 45, 45, 45, 45, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 45, 45, 45, 45, 20, 6, 6, 6, 6] 47 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/26 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347524608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524608 none O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 46, 46, 46, 46, 46, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 46, 46, 46, 46, 20, 6, 6, 6, 6] 47 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347524608 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 Building ZINC000347524608 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347524608 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 25) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347524608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524608 none O=C(Nc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 45, 45, 45, 45, 45, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 45, 45, 45, 45, 20, 6, 6, 6, 6] 47 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 26) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347524608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524608 none O=C(Nc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 20, 20, 20, 46, 46, 46, 46, 46, 20, 20, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 46, 46, 46, 46, 20, 6, 6, 6, 6] 47 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347524608 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524608 Building ZINC000347524646 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347524646 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/27 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347524646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524646 none O=C(Nc1nnc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [10, 1, 10, 10, 17, 17, 17, 17, 21, 21, 17, 21, 21, 17, 1, 1, 1, 5, 5, 2, 2, 5, 5, 10, 21, 21, 17, 21, 21, 5, 5, 5, 5] 21 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/28 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccccc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347524646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524646 none O=C(Nc1nnc(c2ccccc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [10, 1, 10, 10, 17, 17, 17, 17, 21, 21, 20, 21, 21, 17, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 21, 21, 21, 21, 21, 5, 5, 5, 5] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347524646 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 Building ZINC000347524646 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347524646 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 27) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nnc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347524646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524646 none O=C(Nc1nnc(c2ccccc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [10, 1, 10, 10, 17, 17, 17, 17, 21, 21, 17, 21, 21, 17, 1, 1, 1, 5, 5, 2, 2, 5, 5, 10, 21, 21, 17, 21, 21, 5, 5, 5, 5] 21 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 28) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nnc(c2ccccc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347524646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347524646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347524646 none O=C(Nc1nnc(c2ccccc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [10, 1, 10, 10, 17, 17, 17, 17, 21, 21, 20, 21, 21, 17, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 21, 21, 21, 21, 21, 5, 5, 5, 5] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347524646 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347524646 Building ZINC000347526728 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347526728 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/29 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(OCC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347526728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347526728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347526728 none CCOc1ccc(OCC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 27, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 30, 30, 30, 30, 30, 11, 11, 40, 40, 40, 40, 40, 4, 3, 3, 3, 3, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/30 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(OCC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347526728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347526728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347526728 none CCOc1ccc(OCC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 11, 11, 11, 11, 11, 27, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 29, 29, 29, 29, 29, 11, 11, 40, 40, 40, 40, 40, 4, 3, 3, 3, 3, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347526728 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 Building ZINC000347526728 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347526728 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 29) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1ccc(OCC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347526728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347526728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347526728 none CCOc1ccc(OCC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 27, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 30, 30, 30, 30, 30, 11, 11, 40, 40, 40, 40, 40, 4, 3, 3, 3, 3, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 30) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1ccc(OCC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347526728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347526728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347526728 none CCOc1ccc(OCC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 11, 11, 11, 11, 11, 27, 40, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 29, 29, 29, 29, 29, 11, 11, 40, 40, 40, 40, 40, 4, 3, 3, 3, 3, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347526728 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347526728 Building ZINC000347527942 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347527942 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/31 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347527942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347527942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000347527942 none COc1cc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 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: [38, 22, 5, 22, 22, 22, 36, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 3, 5, 5, 22, 22, 22, 38, 38, 38, 22, 36, 36, 36, 5, 5, 5, 5, 5, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/32 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347527942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347527942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000347527942 none COc1cc(OC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 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: [38, 23, 5, 23, 23, 23, 36, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 38, 38, 38, 23, 36, 36, 36, 5, 5, 5, 5, 5, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347527942 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 Building ZINC000347527942 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347527942 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 31) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347527942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347527942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000347527942 none COc1cc(OC)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 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: [38, 22, 5, 22, 22, 22, 36, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 3, 5, 5, 22, 22, 22, 38, 38, 38, 22, 36, 36, 36, 5, 5, 5, 5, 5, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 32) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(OC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347527942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347527942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000347527942 none COc1cc(OC)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 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: [38, 23, 5, 23, 23, 23, 36, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 38, 38, 38, 23, 36, 36, 36, 5, 5, 5, 5, 5, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347527942 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347527942 Building ZINC000192583416 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192583416 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/33 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC000192583416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192583416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000192583416 none COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 34, 34, 34, 34] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/34 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC000192583416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192583416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000192583416 none COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 11, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 38, 38, 38, 38] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192583416 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 Building ZINC000192583416 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192583416 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 33) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC000192583416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192583416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000192583416 none COc1cccc2c1CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 2, 12, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 34, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 3, 34, 34, 34, 34] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 34) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC000192583416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192583416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000192583416 none COc1cccc2c1CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 11, 2, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 38, 38, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 38, 38, 38, 38] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192583416 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192583416 Building ZINC000347531096 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347531096 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/35 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccco1)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347531096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347531096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347531096 none O=C(N(Cc1ccco1)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 28, 47, 47, 47, 47, 11, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 47, 47, 47, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/36 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccco1)CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347531096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347531096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347531096 none O=C(N(Cc1ccco1)CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 29, 47, 47, 47, 47, 11, 20, 20, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 47, 47, 47, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347531096 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 Building ZINC000347531096 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347531096 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 35) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N(Cc1ccco1)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347531096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347531096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347531096 none O=C(N(Cc1ccco1)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 28, 47, 47, 47, 47, 11, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 47, 47, 47, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 36) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N(Cc1ccco1)CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347531096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347531096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347531096 none O=C(N(Cc1ccco1)CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 29, 47, 47, 47, 47, 11, 20, 20, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 47, 47, 47, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347531096 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347531096 Building ZINC000347552359 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347552359 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/37 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347552359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347552359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347552359 none O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 28, 28, 21, 21, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 13, 13, 28, 28, 50, 50, 50, 50, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/38 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347552359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347552359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347552359 none O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 29, 29, 13, 19, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 13, 13, 29, 29, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347552359 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 Building ZINC000347552359 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347552359 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 37) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347552359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347552359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347552359 none O=C(NCc1ccc(c2cccnc2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 28, 28, 21, 21, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 13, 13, 28, 28, 50, 50, 50, 50, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 38) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347552359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347552359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347552359 none O=C(NCc1ccc(c2cccnc2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 13, 29, 29, 13, 19, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 13, 13, 29, 29, 50, 50, 50, 50, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347552359 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347552359 Building ZINC000347553164 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347553164 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/39 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347553164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553164 none COc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 50, 29, 13, 4, 13, 13, 2, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/40 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347553164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553164 none COc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 40, 49, 49, 31, 17, 7, 17, 17, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 49, 49, 49, 49, 31, 31, 17, 17, 17, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347553164 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 Building ZINC000347553164 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347553164 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 39) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347553164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553164 none COc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 50, 29, 13, 4, 13, 13, 2, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 40) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347553164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553164 none COc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 40, 49, 49, 31, 17, 7, 17, 17, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 49, 49, 49, 49, 31, 31, 17, 17, 17, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347553164 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553164 Building ZINC000347553165 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347553165 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/41 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347553165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553165 none COc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 40, 49, 49, 30, 17, 7, 17, 17, 4, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 49, 49, 49, 49, 30, 30, 17, 17, 17, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/42 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347553165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553165 none COc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 50, 30, 13, 4, 13, 13, 2, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 30, 30, 13, 13, 13, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347553165 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 Building ZINC000347553165 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347553165 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 41) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347553165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553165 none COc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 40, 49, 49, 30, 17, 7, 17, 17, 4, 7, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 49, 49, 49, 49, 30, 30, 17, 17, 17, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 42) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347553165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347553165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347553165 none COc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 50, 30, 13, 4, 13, 13, 2, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 30, 30, 13, 13, 13, 4, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347553165 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347553165 Building ZINC000347554190 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347554190 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/43 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347554190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554190 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 12, 12, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/44 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347554190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554190 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 49, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347554190 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 Building ZINC000347554190 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347554190 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 43) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347554190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554190 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 12, 12, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 44) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347554190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554190 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 49, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347554190 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554190 Building ZINC000347554192 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347554192 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/45 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347554192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554192 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 49, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/46 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347554192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554192 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347554192 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 Building ZINC000347554192 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347554192 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 45) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347554192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554192 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 49, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 46) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)Oc1ccc(Cl)cc1) `ZINC000347554192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347554192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347554192 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347554192 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347554192 Building ZINC000347555769 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555769 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/47 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555769 none O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 49, 49, 49, 44, 49, 49, 49, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 21, 21, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/48 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555769 none O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 22, 47, 47, 47, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 22, 22, 47, 44, 47, 5, 5, 5, 5] 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555769 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 Building ZINC000347555769 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555769 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 47) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555769 none O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 49, 49, 49, 44, 49, 49, 49, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 21, 21, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 48) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555769 none O=C(N[C@@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 22, 47, 47, 47, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 22, 22, 47, 44, 47, 5, 5, 5, 5] 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]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555769 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555769 Building ZINC000347555780 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555780 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/49 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555780 none O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 23, 23, 23, 23, 23, 44, 44, 44, 23, 44, 44, 44, 1, 1, 1, 5, 5, 2, 2, 5, 5, 6, 23, 23, 44, 33, 44, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/50 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555780 none O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 28, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 22, 22, 47, 43, 47, 6, 6, 6, 6] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555780 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 Building ZINC000347555780 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555780 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 49) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555780.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555780 none O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 23, 23, 23, 23, 23, 44, 44, 44, 23, 44, 44, 44, 1, 1, 1, 5, 5, 2, 2, 5, 5, 6, 23, 23, 44, 33, 44, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 50) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555780.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555780 none O=C(N[C@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 28, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 22, 22, 47, 43, 47, 6, 6, 6, 6] 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555780 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555780 Building ZINC000347555781 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555781 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/51 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555781 none O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 36, 47, 47, 47, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 22, 22, 47, 36, 47, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/52 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555781 none O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 34, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 46, 36, 46, 5, 5, 5, 5] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555781 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 Building ZINC000347555781 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555781 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 51) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555781 none O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 36, 47, 47, 47, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 22, 22, 47, 36, 47, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 52) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555781 none O=C(N[C@H]1C[C@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 34, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 46, 36, 46, 5, 5, 5, 5] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555781 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555781 Building ZINC000347555782 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555782 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/53 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555782 none O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 36, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 46, 46, 46, 5, 5, 5, 5] 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/54 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555782 none O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 36, 47, 47, 47, 1, 1, 1, 5, 5, 1, 5, 5, 5, 6, 22, 22, 47, 45, 47, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555782 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 Building ZINC000347555782 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347555782 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 53) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555782 none O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 46, 46, 46, 36, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 46, 46, 46, 5, 5, 5, 5] 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 54) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347555782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347555782 none O=C(N[C@@H]1C[C@@H]1c1c(F)cccc1Cl)[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', 'H', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 15, 1, 1, 1, 1, 16, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 47, 47, 47, 36, 47, 47, 47, 1, 1, 1, 5, 5, 1, 5, 5, 5, 6, 22, 22, 47, 45, 47, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347555782 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347555782 Building ZINC000347557611 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347557611 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/55 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(Oc2cccnn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347557611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347557611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347557611 none O=C(Nc1cccc(Oc2cccnn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 39, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/56 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(Oc2cccnn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347557611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347557611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347557611 none O=C(Nc1cccc(Oc2cccnn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 39, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347557611 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 Building ZINC000347557611 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347557611 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 55) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(Oc2cccnn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347557611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347557611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347557611 none O=C(Nc1cccc(Oc2cccnn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 39, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 56) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(Oc2cccnn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347557611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347557611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347557611 none O=C(Nc1cccc(Oc2cccnn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 9, 39, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347557611 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347557611 Building ZINC000347559305 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559305 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/57 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/58 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/59 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/59' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/60 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/60' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559305 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 Building ZINC000347559305 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559305 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 57) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 58) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 59) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 60) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559305 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 Building ZINC000347559305 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559305 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 57) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 58) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 59) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 60) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559305 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 Building ZINC000347559305 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559305 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 57) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 58) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 2, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 21 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 59) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 60) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559305 none C[C@@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 20, 2, 20, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5] 29 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559305 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559305 Building ZINC000347559306 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559306 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/61 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/62 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/63 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/63' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/64 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/64' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559306 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 Building ZINC000347559306 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559306 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 61) grep: /scratch/xiaobo/318708/xbg-8058115.33/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]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 62) grep: /scratch/xiaobo/318708/xbg-8058115.33/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]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 63) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 64) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559306 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 Building ZINC000347559306 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559306 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 61) grep: /scratch/xiaobo/318708/xbg-8058115.33/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]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 62) grep: /scratch/xiaobo/318708/xbg-8058115.33/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]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 63) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 64) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559306 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 Building ZINC000347559306 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347559306 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 61) grep: /scratch/xiaobo/318708/xbg-8058115.33/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]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 62) grep: /scratch/xiaobo/318708/xbg-8058115.33/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]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 2, 19, 1, 1, 1, 3, 3, 1, 2, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 28 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 63) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 64) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347559306.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347559306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347559306 none C[C@H]1CCN(C)c2ccccc2N1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 2, 17, 1, 1, 1, 3, 3, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3] 22 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347559306 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347559306 Building ZINC000347560387 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347560387 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/65 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347560387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347560387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347560387 none COC(=O)C(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 9, 28, 28, 5, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 28, 28, 28, 28, 28, 28, 10, 10, 2, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/66 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347560387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347560387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347560387 none COC(=O)C(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 49, 2, 16, 16, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 19, 16, 20, 20, 20, 16, 10, 10, 2, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347560387 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 Building ZINC000347560387 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347560387 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 65) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)C(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347560387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347560387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347560387 none COC(=O)C(C)(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 9, 28, 28, 5, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 28, 28, 28, 28, 28, 28, 10, 10, 2, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 66) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)C(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347560387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347560387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347560387 none COC(=O)C(C)(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 49, 2, 16, 16, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 19, 16, 20, 20, 20, 16, 10, 10, 2, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347560387 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560387 Building ZINC000347560394 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347560394 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/67 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347560394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560394 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/68 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347560394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560394 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 32, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347560394 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 Building ZINC000347560394 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347560394 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 67) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347560394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560394 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 68) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347560394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560394 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 32, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347560394 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560394 Building ZINC000347560395 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347560395 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/69 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347560395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560395 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 32, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/70 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347560395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560395 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347560395 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 Building ZINC000347560395 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347560395 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 69) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347560395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560395 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 32, 50, 50, 50, 50, 50, 50, 20, 20, 20, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 70) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)c1) `ZINC000347560395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347560395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347560395 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(Cl)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 34, 50, 50, 50, 50, 50, 50, 20, 20, 20, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347560395 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347560395 Building ZINC000347547995 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347547995 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/71 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347547995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547995 none O=C(N1CC[C@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 12, 28, 49, 50, 50, 50, 50, 50, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 12, 12, 49, 49, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 17, 18, 19] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/72 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347547995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547995 none O=C(N1CC[C@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 9, 25, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347547995 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 Building ZINC000347547995 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347547995 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 71) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CC[C@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347547995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547995 none O=C(N1CC[C@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 12, 28, 49, 50, 50, 50, 50, 50, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 12, 12, 49, 49, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 17, 18, 19] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 72) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CC[C@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347547995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547995 none O=C(N1CC[C@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 9, 25, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347547995 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547995 Building ZINC000347547996 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347547996 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/73 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347547996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547996 none O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 9, 24, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/74 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347547996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547996 none O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 12, 28, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347547996 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 Building ZINC000347547996 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347547996 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 73) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347547996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547996 none O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 9, 24, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 74) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347547996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347547996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347547996 none O=C(N1CC[C@@H](COCc2ccccc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 2, 2, 2, 2, 12, 28, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/318708/xbg-8058115.33/working/building/ZINC000347547996 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347547996 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347547996 Building ZINC000347564001 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564001 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/75 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564001 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 25, 25, 26, 50, 50, 50, 50, 50, 25, 25, 4, 4, 4, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/76 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564001 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 3, 3, 3, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564001 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 Building ZINC000347564001 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564001 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 75) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564001 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 25, 25, 26, 50, 50, 50, 50, 50, 25, 25, 4, 4, 4, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 76) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564001 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 3, 3, 3, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564001 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564001 Building ZINC000347564002 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564002 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/77 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564002 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 3, 3, 3, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/78 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564002 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 25, 25, 27, 50, 50, 50, 50, 50, 25, 25, 4, 4, 4, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564002 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 Building ZINC000347564002 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564002 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 77) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564002 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 3, 3, 3, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 78) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1) `ZINC000347564002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347564002 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc(C2CCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 2, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 25, 25, 27, 50, 50, 50, 50, 50, 25, 25, 4, 4, 4, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564002 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564002 Building ZINC000347564129 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564129 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/79 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564129 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 20, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 48, 48, 48, 48, 48, 48, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 48, 48, 48, 48] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/80 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564129 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 20, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 47, 47, 47, 47, 47, 47, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564129 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 Building ZINC000347564129 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564129 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 79) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564129 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 20, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 48, 48, 48, 48, 48, 48, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 48, 48, 48, 48] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 80) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564129 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 20, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 47, 47, 47, 47, 47, 47, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564129 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564129 Building ZINC000347564130 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564130 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/81 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564130 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 20, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 47, 47, 47, 47, 47, 47, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/82 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564130 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 20, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 48, 48, 48, 48, 48, 48, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 48, 48, 48, 48] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564130 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 Building ZINC000347564130 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564130 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 81) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564130 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 44, 20, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 47, 47, 47, 47, 47, 47, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 82) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1) `ZINC000347564130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347564130 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 20, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 48, 48, 48, 48, 48, 48, 49, 49, 49, 20, 20, 4, 3, 3, 3, 3, 48, 48, 48, 48] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564130 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564130 Building ZINC000347564132 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564132 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/83 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347564132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347564132 none Cc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 26, 48, 48, 48, 48, 26, 26, 26, 5, 5, 5, 5, 5, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/84 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347564132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347564132 none Cc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 25, 25, 25, 25, 25, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 47, 47, 47, 47, 25, 25, 25, 5, 5, 5, 5, 5, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564132 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 Building ZINC000347564132 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347564132 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 83) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347564132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347564132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347564132 none Cc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 26, 48, 48, 48, 48, 26, 26, 26, 5, 5, 5, 5, 5, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 84) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347564132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347564132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347564132 none Cc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 25, 25, 25, 25, 25, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 47, 47, 47, 47, 25, 25, 25, 5, 5, 5, 5, 5, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347564132 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347564132 Building ZINC000347565593 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565593 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/85 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C) `ZINC000347565593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565593 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 4, 1, 4, 1, 1, 1, 5, 5, 2, 2, 5, 5, 10, 14, 14, 14, 14, 14, 35, 41, 14, 14, 14, 19, 19, 19, 19, 19, 14, 14, 5, 5, 5, 5, 14, 14, 41, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/86 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C) `ZINC000347565593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565593 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 33, 40, 15, 15, 15, 18, 18, 18, 18, 18, 14, 14, 5, 5, 5, 5, 15, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565593 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 Building ZINC000347565593 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565593 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 85) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C) `ZINC000347565593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565593 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 4, 1, 4, 1, 1, 1, 5, 5, 2, 2, 5, 5, 10, 14, 14, 14, 14, 14, 35, 41, 14, 14, 14, 19, 19, 19, 19, 19, 14, 14, 5, 5, 5, 5, 14, 14, 41, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 86) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C) `ZINC000347565593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565593 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 15, 15, 15, 15, 15, 33, 40, 15, 15, 15, 18, 18, 18, 18, 18, 14, 14, 5, 5, 5, 5, 15, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565593 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565593 Building ZINC000347565595 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565595 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/87 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C) `ZINC000347565595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565595 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 19, 19, 19, 19, 19, 39, 45, 19, 19, 19, 21, 21, 21, 21, 21, 16, 16, 4, 4, 4, 4, 19, 19, 45, 45, 45, 45, 45, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/88 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C) `ZINC000347565595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565595 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 17, 17, 17, 17, 17, 37, 41, 17, 17, 17, 21, 21, 21, 21, 21, 17, 17, 5, 5, 5, 5, 17, 17, 41, 41, 41, 41, 41, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565595 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 Building ZINC000347565595 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565595 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 87) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C) `ZINC000347565595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565595 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 19, 19, 19, 19, 19, 39, 45, 19, 19, 19, 21, 21, 21, 21, 21, 16, 16, 4, 4, 4, 4, 19, 19, 45, 45, 45, 45, 45, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 88) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C) `ZINC000347565595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565595 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 17, 17, 17, 17, 17, 37, 41, 17, 17, 17, 21, 21, 21, 21, 21, 17, 17, 5, 5, 5, 5, 17, 17, 41, 41, 41, 41, 41, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565595 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565595 Building ZINC000347565597 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565597 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/89 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565597 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 17, 17, 17, 17, 17, 39, 43, 17, 17, 17, 21, 21, 21, 21, 21, 16, 16, 5, 5, 5, 5, 17, 17, 43, 43, 43, 43, 43, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/90 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565597 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 9, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 18, 18, 18, 18, 18, 38, 43, 18, 18, 18, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 4, 18, 18, 43, 43, 43, 43, 43, 18, 18, 18, 18, 18, 18] 49 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565597 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 Building ZINC000347565597 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565597 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 89) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565597 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 17, 17, 17, 17, 17, 39, 43, 17, 17, 17, 21, 21, 21, 21, 21, 16, 16, 5, 5, 5, 5, 17, 17, 43, 43, 43, 43, 43, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 90) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565597 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 9, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 18, 18, 18, 18, 18, 38, 43, 18, 18, 18, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 4, 18, 18, 43, 43, 43, 43, 43, 18, 18, 18, 18, 18, 18] 49 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565597 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565597 Building ZINC000347565598 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565598 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/91 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565598 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 14, 14, 14, 14, 14, 35, 43, 14, 14, 14, 17, 17, 17, 17, 17, 13, 13, 5, 5, 5, 5, 14, 14, 43, 43, 43, 43, 43, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/92 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565598 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 14, 14, 14, 14, 14, 35, 41, 14, 14, 14, 19, 19, 19, 19, 19, 14, 14, 5, 5, 5, 5, 14, 14, 41, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565598 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 Building ZINC000347565598 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347565598 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 91) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347565598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565598 none CCCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 14, 14, 14, 14, 14, 35, 43, 14, 14, 14, 17, 17, 17, 17, 17, 13, 13, 5, 5, 5, 5, 14, 14, 43, 43, 43, 43, 43, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 92) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C) `ZINC000347565598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347565598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347565598 none CCCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1C[C@@H](OCC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 14, 14, 14, 14, 14, 35, 41, 14, 14, 14, 19, 19, 19, 19, 19, 14, 14, 5, 5, 5, 5, 14, 14, 41, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347565598 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347565598 Building ZINC000347571378 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347571378 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/93 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347571378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347571378 none CCc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 30, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/94 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347571378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347571378 none CCc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 28, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571378 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 Building ZINC000347571378 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347571378 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 93) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347571378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347571378 none CCc1nnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 30, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 94) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1) `ZINC000347571378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347571378 none CCc1nnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 28, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571378 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571378 Building ZINC000347571380 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347571380 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/95 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571380 none C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 28, 2, 28, 1, 1, 1, 4, 4, 1, 1, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 40, 40] 43 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/96 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571380 none C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 2, 27, 1, 1, 1, 3, 3, 1, 2, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 40, 40] 44 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571380 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 Building ZINC000347571380 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347571380 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 95) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571380 none C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 28, 2, 28, 1, 1, 1, 4, 4, 1, 1, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 40, 40] 43 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 96) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571380 none C[C@@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 2, 27, 1, 1, 1, 3, 3, 1, 2, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3, 40, 40] 44 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571380 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571380 Building ZINC000347571382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347571382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/97 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/98 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/99 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/99' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/100 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/100' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 Building ZINC000347571382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347571382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 97) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 98) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 99) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 100) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 Building ZINC000347571382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347571382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 97) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 98) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 99) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 100) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 Building ZINC000347571382 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347571382 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 97) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 98) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 3, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 99) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 100) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347571382.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347571382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347571382 none C[C@H]1CN(C)c2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 3, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 3, 36, 36] 39 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 81 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347571382 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347571382 Building ZINC000347573161 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347573161 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/101 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347573161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573161 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 34, 34, 12, 12, 50, 50, 50, 50, 34, 34, 10, 10, 10, 6, 3, 3, 3, 3, 34, 34, 50, 50, 50, 34, 34] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/102 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347573161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573161 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 31, 31, 14, 14, 50, 50, 50, 50, 31, 31, 11, 11, 11, 6, 3, 3, 3, 3, 31, 31, 50, 50, 50, 31, 31] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347573161 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 Building ZINC000347573161 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347573161 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 101) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347573161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573161 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 34, 34, 12, 12, 50, 50, 50, 50, 34, 34, 10, 10, 10, 6, 3, 3, 3, 3, 34, 34, 50, 50, 50, 34, 34] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 102) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347573161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573161 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 31, 31, 14, 14, 50, 50, 50, 50, 31, 31, 11, 11, 11, 6, 3, 3, 3, 3, 31, 31, 50, 50, 50, 31, 31] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347573161 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573161 Building ZINC000347573163 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347573163 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/103 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347573163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573163 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 31, 31, 13, 13, 50, 50, 50, 50, 31, 31, 11, 11, 11, 6, 3, 3, 3, 3, 31, 31, 50, 50, 50, 31, 31] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 156 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/104 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347573163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573163 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 36, 36, 12, 15, 50, 50, 50, 50, 36, 36, 11, 11, 11, 6, 3, 3, 3, 3, 36, 36, 50, 50, 50, 36, 36] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347573163 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 Building ZINC000347573163 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347573163 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 103) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347573163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573163 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 31, 31, 13, 13, 50, 50, 50, 50, 31, 31, 11, 11, 11, 6, 3, 3, 3, 3, 31, 31, 50, 50, 50, 31, 31] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 156 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 104) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1) `ZINC000347573163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347573163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347573163 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(n2cccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 36, 36, 12, 15, 50, 50, 50, 50, 36, 36, 11, 11, 11, 6, 3, 3, 3, 3, 36, 36, 50, 50, 50, 36, 36] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347573163 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347573163 Building ZINC000347574185 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347574185 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/105 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347574185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347574185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347574185 none O=C(NCc1c(F)cccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 34, 34, 34, 34, 34, 34, 34, 43, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 15, 15, 34, 34, 34, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/106 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347574185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347574185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347574185 none O=C(NCc1c(F)cccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 34, 34, 34, 17, 34, 34, 34, 43, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 15, 15, 34, 34, 34, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347574185 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 Building ZINC000347574185 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347574185 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 105) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1c(F)cccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347574185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347574185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347574185 none O=C(NCc1c(F)cccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 34, 34, 34, 34, 34, 34, 34, 43, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 15, 15, 34, 34, 34, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 106) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1c(F)cccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347574185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347574185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347574185 none O=C(NCc1c(F)cccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 34, 34, 34, 17, 34, 34, 34, 43, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 15, 15, 34, 34, 34, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347574185 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347574185 Building ZINC000347575906 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347575906 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/107 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347575906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575906 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 42, 50, 50, 42, 50, 50, 50, 23, 23, 23, 14, 14, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/108 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347575906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575906 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 50, 50, 39, 50, 50, 50, 21, 21, 21, 13, 13, 4, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347575906 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 Building ZINC000347575906 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347575906 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 107) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347575906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575906 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 42, 50, 50, 42, 50, 50, 50, 23, 23, 23, 14, 14, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 108) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347575906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575906 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 50, 50, 39, 50, 50, 50, 21, 21, 21, 13, 13, 4, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347575906 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575906 Building ZINC000347575909 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347575909 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/109 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347575909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575909 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 50, 50, 39, 50, 50, 50, 21, 21, 21, 12, 12, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/110 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347575909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575909 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 42, 50, 50, 42, 50, 50, 50, 23, 23, 23, 14, 14, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347575909 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 Building ZINC000347575909 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347575909 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 109) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347575909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575909 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 50, 50, 39, 50, 50, 50, 21, 21, 21, 12, 12, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 110) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl) `ZINC000347575909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347575909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347575909 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 42, 50, 50, 42, 50, 50, 50, 23, 23, 23, 14, 14, 3, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347575909 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347575909 Building ZINC000347580210 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347580210 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/111 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347580210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580210 none COc1ccccc1[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 46, 46, 17, 17, 17, 17, 17, 2, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 50, 50, 50, 46, 46, 46, 46, 17, 17, 17, 17, 2, 2, 2, 2, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/112 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347580210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580210 none COc1ccccc1[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 38, 46, 46, 15, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 50, 50, 50, 46, 46, 46, 46, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347580210 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 Building ZINC000347580210 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347580210 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 111) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347580210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580210 none COc1ccccc1[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 46, 46, 17, 17, 17, 17, 17, 2, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 50, 50, 50, 46, 46, 46, 46, 17, 17, 17, 17, 2, 2, 2, 2, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 112) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347580210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580210 none COc1ccccc1[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 38, 46, 46, 15, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 50, 50, 50, 46, 46, 46, 46, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347580210 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580210 Building ZINC000347580211 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347580211 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/113 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347580211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580211 none COc1ccccc1[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 36, 47, 47, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 50, 50, 50, 47, 47, 47, 47, 14, 14, 14, 14, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/114 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347580211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580211 none COc1ccccc1[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 46, 46, 15, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 50, 50, 50, 46, 46, 46, 46, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347580211 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 Building ZINC000347580211 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347580211 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 113) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347580211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580211 none COc1ccccc1[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 36, 47, 47, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 50, 50, 50, 47, 47, 47, 47, 14, 14, 14, 14, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 114) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000347580211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347580211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347580211 none COc1ccccc1[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 46, 46, 15, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 50, 50, 50, 46, 46, 46, 46, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347580211 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347580211 Building ZINC000347602561 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347602561 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/115 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000347602561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347602561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602561 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 18, 18, 34, 39, 18, 25, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 2, 2, 2, 2, 34, 34, 39, 39, 39, 25, 25, 26, 26, 26, 26, 26] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/116 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000347602561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347602561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602561 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 15, 15, 31, 41, 15, 26, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 2, 2, 2, 2, 31, 31, 41, 41, 41, 26, 26, 29, 29, 29, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347602561 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 Building ZINC000347602561 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347602561 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 115) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000347602561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347602561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602561 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 18, 18, 34, 39, 18, 25, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 2, 2, 2, 2, 34, 34, 39, 39, 39, 25, 25, 26, 26, 26, 26, 26] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 215 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 116) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000347602561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347602561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602561 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 15, 15, 31, 41, 15, 26, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 2, 2, 2, 2, 31, 31, 41, 41, 41, 26, 26, 29, 29, 29, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 234 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347602561 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602561 Building ZINC000347602563 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347602563 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/117 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1) `ZINC000347602563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347602563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602563 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 15, 15, 31, 41, 15, 26, 29, 29, 26, 29, 29, 10, 10, 10, 10, 10, 2, 2, 2, 2, 31, 31, 41, 41, 41, 26, 26, 29, 29, 29, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/118 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1) `ZINC000347602563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347602563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602563 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 18, 18, 34, 39, 18, 25, 26, 26, 25, 26, 26, 11, 11, 11, 11, 11, 2, 2, 2, 2, 34, 34, 39, 39, 39, 25, 25, 26, 26, 26, 26, 26] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347602563 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 Building ZINC000347602563 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347602563 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 117) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1) `ZINC000347602563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347602563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602563 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 15, 15, 31, 41, 15, 26, 29, 29, 26, 29, 29, 10, 10, 10, 10, 10, 2, 2, 2, 2, 31, 31, 41, 41, 41, 26, 26, 29, 29, 29, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 118) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1) `ZINC000347602563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347602563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000347602563 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 18, 18, 34, 39, 18, 25, 26, 26, 25, 26, 26, 11, 11, 11, 11, 11, 2, 2, 2, 2, 34, 34, 39, 39, 39, 25, 25, 26, 26, 26, 26, 26] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347602563 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602563 Building ZINC000347602580 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347602580 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/119 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347602580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347602580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347602580 none O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 14, 34, 34, 34, 34, 34, 49, 49, 34, 47, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 34, 34, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/120 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347602580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347602580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347602580 none O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 14, 34, 34, 34, 34, 34, 49, 49, 45, 45, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 34, 34, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347602580 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 Building ZINC000347602580 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347602580 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 119) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347602580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347602580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347602580 none O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 14, 34, 34, 34, 34, 34, 49, 49, 34, 47, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 34, 34, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 120) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347602580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347602580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347602580 none O=C(Nc1ccnn1c1ccc(Cl)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 14, 34, 34, 34, 34, 34, 49, 49, 45, 45, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 34, 34, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347602580 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347602580 Building ZINC000347584914 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347584914 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/121 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347584914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347584914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347584914 none O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 16, 16, 36, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 16, 16, 16, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/122 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347584914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347584914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347584914 none O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 10, 15, 15, 15, 15, 35, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 15, 15, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347584914 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 Building ZINC000347584914 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347584914 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 121) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347584914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347584914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347584914 none O=C(Nc1ccc(F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 16, 16, 36, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 16, 16, 16, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 122) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347584914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347584914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347584914 none O=C(Nc1ccc(F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 10, 15, 15, 15, 15, 35, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 15, 15, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347584914 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584914 Building ZINC000347584992 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347584992 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/123 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1) `ZINC000347584992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347584992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347584992 none Cc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 50, 50, 16, 16, 16, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 50, 50, 50, 50, 26, 50, 50, 16, 9, 3, 3, 3, 3, 16, 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/124 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1) `ZINC000347584992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347584992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347584992 none Cc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 50, 50, 16, 16, 16, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 50, 50, 50, 50, 49, 50, 50, 16, 9, 3, 3, 3, 3, 16, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347584992 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 Building ZINC000347584992 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347584992 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 123) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1) `ZINC000347584992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347584992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347584992 none Cc1ccccc1c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 50, 50, 16, 16, 16, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 50, 50, 50, 50, 26, 50, 50, 16, 9, 3, 3, 3, 3, 16, 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 124) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1) `ZINC000347584992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347584992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347584992 none Cc1ccccc1c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 50, 50, 16, 16, 16, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 50, 50, 50, 50, 49, 50, 50, 16, 9, 3, 3, 3, 3, 16, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347584992 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347584992 Building ZINC000347587399 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587399 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/125 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587399 none Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 15, 38, 38, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 38, 38, 38, 38, 15, 38, 38, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/126 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587399 none Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 17, 45, 45, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 17, 45, 45, 45, 45, 17, 45, 45, 17, 17, 4, 4, 4, 4, 17, 17, 17, 17, 17] 48 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587399 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 Building ZINC000347587399 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587399 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 125) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587399 none Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 15, 38, 38, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 38, 38, 38, 38, 15, 38, 38, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 126) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587399 none Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 17, 45, 45, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 17, 45, 45, 45, 45, 17, 45, 45, 17, 17, 4, 4, 4, 4, 17, 17, 17, 17, 17] 48 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587399 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587399 Building ZINC000347587406 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587406 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/127 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587406 none Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 33, 47, 47, 21, 21, 21, 21, 12, 1, 12, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 21, 21, 47, 47, 47, 47, 44, 47, 47, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21, 21] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/128 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587406 none Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 43, 44, 44, 20, 20, 20, 20, 13, 1, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 44, 44, 44, 44, 43, 44, 44, 20, 20, 4, 4, 4, 4, 20, 20, 20, 20, 20] 47 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587406 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 Building ZINC000347587406 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587406 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 127) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587406 none Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 33, 47, 47, 21, 21, 21, 21, 12, 1, 12, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 21, 21, 21, 47, 47, 47, 47, 44, 47, 47, 21, 21, 4, 4, 4, 4, 21, 21, 21, 21, 21] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 142 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 128) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587406 none Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [44, 44, 44, 43, 44, 44, 20, 20, 20, 20, 13, 1, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 44, 44, 44, 44, 43, 44, 44, 20, 20, 4, 4, 4, 4, 20, 20, 20, 20, 20] 47 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587406 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587406 Building ZINC000347587415 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587415 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/129 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587415 none Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 28, 47, 47, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 47, 47, 47, 47, 42, 47, 47, 22, 22, 4, 4, 4, 4, 22, 22, 22, 22, 22] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/130 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587415 none Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 29, 29, 29, 29, 19, 3, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 29, 29, 29, 49, 49, 49, 49, 46, 49, 49, 29, 29, 4, 4, 4, 4, 29, 29, 29, 29, 29] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587415 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 Building ZINC000347587415 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587415 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 129) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587415 none Cc1ccccc1[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 28, 47, 47, 22, 22, 22, 22, 16, 2, 16, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 47, 47, 47, 47, 42, 47, 47, 22, 22, 4, 4, 4, 4, 22, 22, 22, 22, 22] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 130) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1) `ZINC000347587415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587415 none Cc1ccccc1[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 29, 29, 29, 29, 19, 3, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 29, 29, 29, 29, 29, 49, 49, 49, 49, 46, 49, 49, 29, 29, 4, 4, 4, 4, 29, 29, 29, 29, 29] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587415 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587415 Building ZINC000347587426 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587426 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/131 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587426 none Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 48, 48, 22, 22, 22, 22, 15, 3, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 48, 48, 48, 48, 22, 48, 48, 22, 22, 4, 4, 4, 4, 22, 22, 22, 22, 22] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/132 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587426 none Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 19, 47, 47, 19, 19, 19, 19, 14, 4, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 19, 19, 19, 19, 19, 47, 47, 47, 47, 20, 47, 47, 19, 19, 4, 4, 4, 4, 19, 19, 19, 19, 19] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587426 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 Building ZINC000347587426 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347587426 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 131) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347587426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587426 none Cc1ccccc1[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 48, 48, 22, 22, 22, 22, 15, 3, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 48, 48, 48, 48, 22, 48, 48, 22, 22, 4, 4, 4, 4, 22, 22, 22, 22, 22] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 132) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1) `ZINC000347587426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347587426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347587426 none Cc1ccccc1[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](C)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 19, 47, 47, 19, 19, 19, 19, 14, 4, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 19, 19, 19, 19, 19, 47, 47, 47, 47, 20, 47, 47, 19, 19, 4, 4, 4, 4, 19, 19, 19, 19, 19] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347587426 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347587426 Building ZINC000347589728 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347589728 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/133 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/134 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/135 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/135' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/136 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/136' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347589728 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 Building ZINC000347589728 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347589728 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 133) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 134) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 135) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 136) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347589728 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 Building ZINC000347589728 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347589728 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 133) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 134) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 135) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 136) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347589728 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 Building ZINC000347589728 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347589728 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 133) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 134) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 15, 21, 21, 21, 21, 38, 50, 50, 21, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 135) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 136) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347589728.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347589728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347589728 none O=C(N1CCN(CC2CC2)c2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 17, 17, 17, 17, 35, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347589728 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347589728 Building ZINC000347600145 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347600145 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/137 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347600145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347600145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347600145 none CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 5, 5, 19, 19, 50, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/138 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347600145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347600145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347600145 none CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 20, 20, 50, 2, 2, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347600145 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 Building ZINC000347600145 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347600145 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 137) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347600145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347600145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347600145 none CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 5, 5, 19, 19, 50, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 138) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347600145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347600145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347600145 none CN(Cc1nc(C(F)(F)F)cs1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 5, 15, 15, 15, 1, 14, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 20, 20, 50, 2, 2, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347600145 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347600145 Building ZINC000347601557 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347601557 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/139 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347601557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347601557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347601557 none O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 21, 21, 21, 21, 21, 21, 28, 35, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 21, 21, 21, 21, 35, 35, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/140 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347601557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347601557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347601557 none O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 21, 21, 21, 21, 21, 21, 31, 36, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 21, 21, 21, 21, 36, 36, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347601557 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 Building ZINC000347601557 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347601557 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 139) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347601557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347601557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347601557 none O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 21, 21, 21, 21, 21, 21, 28, 35, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 21, 21, 21, 21, 35, 35, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 140) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347601557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347601557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347601557 none O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 21, 21, 21, 21, 21, 21, 31, 36, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 21, 21, 21, 21, 36, 36, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347601557 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347601557 Building ZINC000347604073 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347604073 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/141 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604073 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 8, 8, 8, 4, 3, 3, 3, 3, 38, 38, 38, 50, 50, 50, 38] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/142 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604073 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 8, 8, 8, 4, 2, 2, 2, 2, 38, 38, 38, 50, 50, 50, 38] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604073 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 Building ZINC000347604073 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347604073 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 141) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604073 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 8, 8, 8, 4, 3, 3, 3, 3, 38, 38, 38, 50, 50, 50, 38] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 142) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604073 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 8, 8, 8, 4, 2, 2, 2, 2, 38, 38, 38, 50, 50, 50, 38] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604073 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604073 Building ZINC000347604075 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347604075 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/143 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604075 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 39, 39, 39, 39, 39, 50, 50, 50, 50, 39, 8, 8, 8, 4, 2, 2, 2, 2, 39, 39, 39, 50, 50, 50, 39] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/144 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604075 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 8, 8, 8, 4, 3, 3, 3, 3, 38, 38, 38, 50, 50, 50, 38] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604075 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 Building ZINC000347604075 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347604075 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 143) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604075.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604075 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 39, 39, 39, 39, 39, 50, 50, 50, 50, 39, 8, 8, 8, 4, 2, 2, 2, 2, 39, 39, 39, 50, 50, 50, 39] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 144) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1) `ZINC000347604075.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347604075 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 8, 8, 8, 4, 3, 3, 3, 3, 38, 38, 38, 50, 50, 50, 38] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604075 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604075 Building ZINC000347604928 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604928 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/145 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/146 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/147 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/147' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/148 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/148' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604928 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 Building ZINC000347604928 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604928 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 145) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 146) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 147) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 148) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604928 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 Building ZINC000347604928 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604928 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 145) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 146) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 147) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 148) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604928 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 Building ZINC000347604928 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604928 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 145) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 146) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 147) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 39, 39, 48, 50, 50, 48, 50, 50, 21, 21, 21, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 148) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604928 none C[C@@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604928 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604928 Building ZINC000347604929 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604929 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/149 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/150 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/151 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/151' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/152 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/152' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604929 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 Building ZINC000347604929 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604929 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 149) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 150) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 151) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 152) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604929 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 Building ZINC000347604929 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604929 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 149) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 150) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 151) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 152) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604929 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 Building ZINC000347604929 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347604929 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 149) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 150) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 151) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 26, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 40, 40, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 16, 11, 11, 2, 2, 2, 2, 2, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 152) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])c1ccc(F)cc1)N(C)Cc1ccccc1) `ZINC000347604929.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347604929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000347604929 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)N(C)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 10, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 39, 39, 48, 50, 50, 50, 50, 50, 22, 22, 22, 14, 14, 9, 9, 2, 2, 2, 2, 2, 39, 39, 39, 48, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604929 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604929 Building ZINC000347604955 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347604955 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/153 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br) `ZINC000347604955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347604955 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 15, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 10, 6, 6, 6, 6, 18, 18] 20 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/154 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br) `ZINC000347604955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347604955 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 15, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 10, 6, 6, 6, 6, 18, 18] 20 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604955 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 Building ZINC000347604955 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347604955 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 153) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br) `ZINC000347604955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347604955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347604955 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 15, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 10, 6, 6, 6, 6, 18, 18] 20 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 154) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br) `ZINC000347604955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347604955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347604955 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 15, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 6, 6, 1, 1, 6, 6, 18, 18, 18, 18, 18, 18, 18, 10, 6, 6, 6, 6, 18, 18] 20 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347604955 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347604955 Building ZINC000347606044 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347606044 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/155 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1) `ZINC000347606044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347606044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347606044 none CCc1nnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 23, 14, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 37, 50, 50, 50, 50, 50, 23, 23, 4, 5, 5, 5, 5, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/156 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1) `ZINC000347606044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347606044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347606044 none CCc1nnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 6, 6, 24, 24, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 24, 24, 39, 50, 50, 50, 50, 50, 24, 24, 4, 4, 4, 4, 4, 24, 24] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347606044 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 Building ZINC000347606044 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347606044 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 155) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1nnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1) `ZINC000347606044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347606044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347606044 none CCc1nnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 23, 14, 23, 23, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 37, 50, 50, 50, 50, 50, 23, 23, 4, 5, 5, 5, 5, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 156) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1nnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1) `ZINC000347606044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347606044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347606044 none CCc1nnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 6, 6, 24, 24, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 24, 24, 39, 50, 50, 50, 50, 50, 24, 24, 4, 4, 4, 4, 4, 24, 24] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347606044 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606044 Building ZINC000347606899 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347606899 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/157 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1cccc(F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347606899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347606899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347606899 none O=C(N(c1cccc(F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 26, 26, 26, 26, 26, 26, 8, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 1, 3, 4, 4, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4] 35 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/158 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1cccc(F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347606899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347606899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347606899 none O=C(N(c1cccc(F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 30, 30, 30, 30, 30, 30, 8, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5] 41 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347606899 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 Building ZINC000347606899 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347606899 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 157) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N(c1cccc(F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347606899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347606899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347606899 none O=C(N(c1cccc(F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 26, 26, 26, 26, 26, 26, 8, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 1, 3, 4, 4, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4] 35 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 158) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N(c1cccc(F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347606899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347606899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347606899 none O=C(N(c1cccc(F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 30, 30, 30, 30, 30, 30, 8, 16, 16, 16, 16, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5] 41 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347606899 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347606899 Building ZINC000347608124 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608124 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/159 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/160 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/161 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/161' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/162 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/162' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608124 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 Building ZINC000347608124 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608124 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 159) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 160) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 161) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 162) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608124 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 Building ZINC000347608124 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608124 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 159) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 160) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 161) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 162) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608124 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 Building ZINC000347608124 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608124 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 159) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 160) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 9, 3, 15, 1, 1, 1, 3, 3, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 19, 19, 19] 21 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 161) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 162) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21) `ZINC000347608124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000347608124 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 12, 3, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 20, 20, 20] 22 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608124 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608124 Building ZINC000347608189 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347608189 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/163 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608189 none O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 16, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 50, 50, 50, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/164 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608189 none O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 3, 19, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 50, 50, 50, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608189 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 Building ZINC000347608189 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347608189 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 163) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608189 none O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 16, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 50, 50, 50, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 164) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608189 none O=C(N1C[C@@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 3, 19, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 50, 50, 50, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608189 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608189 Building ZINC000347608191 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347608191 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/165 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608191 none O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 3, 17, 20, 20, 20, 20, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 49, 49, 49, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/166 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608191 none O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 3, 15, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 50, 50, 50, 18, 18, 18, 18, 18, 18, 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, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608191 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 Building ZINC000347608191 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347608191 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 165) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608191 none O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 3, 17, 20, 20, 20, 20, 49, 49, 49, 49, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 49, 49, 49, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 166) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347608191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347608191 none O=C(N1C[C@H](n2cccn2)Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 3, 15, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 50, 50, 50, 18, 18, 18, 18, 18, 18, 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, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608191 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608191 Building ZINC000347608271 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608271 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/167 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/168 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/169 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/169' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/170 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/170' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608271 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 Building ZINC000347608271 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608271 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 167) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 168) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 169) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 170) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608271 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 Building ZINC000347608271 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608271 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 167) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 168) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 169) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 170) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608271 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 Building ZINC000347608271 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347608271 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 167) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 168) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 25, 2, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 45, 45, 45] 46 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 169) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 170) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21) `ZINC000347608271.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347608271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347608271 none CN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', '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', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 44, 44, 44, 24, 2, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 44, 44, 44] 45 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347608271 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347608271 Building ZINC000347642807 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347642807 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/171 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347642807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347642807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347642807 none COCCCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 41, 23, 7, 7, 7, 5, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 48, 50, 48, 48, 41, 41, 7, 7, 7, 7, 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, 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/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/172 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347642807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347642807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347642807 none COCCCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 24, 8, 8, 8, 5, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 49, 47, 47, 40, 40, 8, 8, 8, 8, 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, 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/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347642807 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 Building ZINC000347642807 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347642807 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 171) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347642807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347642807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347642807 none COCCCOc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 41, 23, 7, 7, 7, 5, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 48, 50, 48, 48, 41, 41, 7, 7, 7, 7, 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, 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/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 172) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347642807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347642807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347642807 none COCCCOc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 40, 24, 8, 8, 8, 5, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 49, 47, 47, 40, 40, 8, 8, 8, 8, 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, 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/318708/xbg-8058115.33/working/building/ZINC000347642807 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347642807 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347642807 Building ZINC000347644289 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347644289 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/173 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccsc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347644289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347644289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347644289 none O=C(Nc1nnc(c2ccsc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 18, 18, 18, 18, 35, 35, 35, 35, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 35, 35, 35, 6, 6, 6, 6] 35 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/174 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(c2ccsc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347644289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347644289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347644289 none O=C(Nc1nnc(c2ccsc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 17, 17, 17, 17, 34, 34, 34, 34, 17, 1, 1, 1, 6, 6, 1, 2, 6, 6, 10, 34, 34, 34, 6, 6, 6, 6] 34 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347644289 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 Building ZINC000347644289 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347644289 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 173) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nnc(c2ccsc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347644289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347644289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347644289 none O=C(Nc1nnc(c2ccsc2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 18, 18, 18, 18, 35, 35, 35, 35, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 35, 35, 35, 6, 6, 6, 6] 35 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 174) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nnc(c2ccsc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347644289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347644289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347644289 none O=C(Nc1nnc(c2ccsc2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 14, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 17, 17, 17, 17, 34, 34, 34, 34, 17, 1, 1, 1, 6, 6, 1, 2, 6, 6, 10, 34, 34, 34, 6, 6, 6, 6] 34 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347644289 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347644289 Building ZINC000347645365 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347645365 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/175 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347645365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347645365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347645365 none O=C(Nc1cc(Cl)ccc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 23, 23, 23, 6, 23, 23, 23, 49, 49, 49, 49, 1, 1, 1, 5, 5, 2, 5, 5, 5, 6, 23, 23, 23, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/176 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347645365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347645365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347645365 none O=C(Nc1cc(Cl)ccc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 23, 23, 23, 13, 23, 23, 23, 50, 50, 50, 50, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347645365 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 Building ZINC000347645365 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347645365 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 175) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347645365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347645365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347645365 none O=C(Nc1cc(Cl)ccc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 23, 23, 23, 6, 23, 23, 23, 49, 49, 49, 49, 1, 1, 1, 5, 5, 2, 5, 5, 5, 6, 23, 23, 23, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 176) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347645365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347645365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347645365 none O=C(Nc1cc(Cl)ccc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 23, 23, 23, 13, 23, 23, 23, 50, 50, 50, 50, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 23, 23, 23, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347645365 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347645365 Building ZINC000347648183 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347648183 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/177 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000347648183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347648183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347648183 none COC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 23, 48, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 23, 23, 48, 48, 48, 23, 23, 5, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/178 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000347648183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347648183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347648183 none COC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 22, 48, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 48, 48, 48, 22, 22, 5, 4, 4, 4, 4, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347648183 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 Building ZINC000347648183 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347648183 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 177) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000347648183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347648183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347648183 none COC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 23, 48, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 23, 23, 48, 48, 48, 23, 23, 5, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 178) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1) `ZINC000347648183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347648183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347648183 none COC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 22, 48, 22, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 48, 48, 48, 22, 22, 5, 4, 4, 4, 4, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347648183 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347648183 Building ZINC000347649133 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347649133 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/179 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347649133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347649133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347649133 none O=C(Nc1ccc(OC(F)F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 10, 10, 37, 50, 50, 10, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 10, 10, 50, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/180 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347649133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347649133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347649133 none O=C(Nc1ccc(OC(F)F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 10, 10, 37, 50, 50, 10, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 10, 10, 50, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347649133 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 Building ZINC000347649133 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347649133 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 179) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC(F)F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347649133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347649133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347649133 none O=C(Nc1ccc(OC(F)F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 10, 10, 37, 50, 50, 10, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 10, 10, 50, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 180) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC(F)F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347649133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347649133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347649133 none O=C(Nc1ccc(OC(F)F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 10, 10, 37, 50, 50, 10, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 10, 10, 50, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347649133 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347649133 Building ZINC000347650175 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347650175 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/181 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347650175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347650175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347650175 none Cc1csc(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 10, 5, 10, 21, 21, 21, 21, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 40, 40, 40, 40, 40, 21, 21, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/182 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347650175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347650175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347650175 none Cc1csc(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 10, 5, 10, 20, 20, 20, 20, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 39, 39, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347650175 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 Building ZINC000347650175 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347650175 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 181) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1csc(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347650175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347650175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347650175 none Cc1csc(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 10, 5, 10, 21, 21, 21, 21, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 40, 40, 40, 40, 40, 21, 21, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 182) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1csc(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347650175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347650175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347650175 none Cc1csc(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 10, 5, 10, 20, 20, 20, 20, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 39, 39, 39, 39, 39, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347650175 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650175 Building ZINC000347650196 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347650196 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/183 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347650196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347650196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347650196 none O=C(Nc1cccnc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 27, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/184 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccnc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347650196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347650196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347650196 none O=C(Nc1cccnc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 16, 16, 26, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347650196 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 Building ZINC000347650196 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347650196 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 183) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccnc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347650196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347650196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347650196 none O=C(Nc1cccnc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 27, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 184) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccnc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347650196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347650196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347650196 none O=C(Nc1cccnc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 16, 16, 26, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347650196 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347650196 Building ZINC000347635601 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635601 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/185 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/186 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/187 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/187' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/188 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/188' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635601 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 Building ZINC000347635601 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635601 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 185) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 186) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 187) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 188) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635601 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 Building ZINC000347635601 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635601 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 185) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 186) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 187) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 188) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635601 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 Building ZINC000347635601 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635601 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 185) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 186) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3] 26 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 187) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 188) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635601.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635601 none O=C(N1C[C@@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3] 27 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635601 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635601 Building ZINC000347635602 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635602 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/189 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/190 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/191 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/191' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/192 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/192' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635602 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 Building ZINC000347635602 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635602 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 189) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 190) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 191) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 192) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635602 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 Building ZINC000347635602 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635602 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 189) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 190) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 191) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 192) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635602 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 Building ZINC000347635602 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347635602 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 189) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 190) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [18, 2, 24, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 2, 1, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 41 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 191) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 192) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347635602.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347635602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347635602 none O=C(N1C[C@H]2CCCN2Cc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 3, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 3, 3, 1, 2, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 3] 36 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347635602 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347635602 Building ZINC000347636270 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347636270 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/193 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(Cl)c1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347636270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347636270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347636270 none O=C(Nc1cccc(Cl)c1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 21, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/194 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(Cl)c1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347636270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347636270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347636270 none O=C(Nc1cccc(Cl)c1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 21, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347636270 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 Building ZINC000347636270 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347636270 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 193) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(Cl)c1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347636270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347636270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347636270 none O=C(Nc1cccc(Cl)c1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 21, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 194) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(Cl)c1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347636270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347636270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347636270 none O=C(Nc1cccc(Cl)c1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 21, 21, 21, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347636270 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347636270 Building ZINC000347637366 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347637366 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/195 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347637366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347637366 none COC(=O)c1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 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: [50, 49, 19, 50, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 3, 5, 5, 50, 50, 50, 19, 19, 19, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/196 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347637366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347637366 none COC(=O)c1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 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: [50, 49, 19, 50, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 19, 19, 19, 6, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347637366 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 Building ZINC000347637366 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347637366 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 195) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347637366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347637366 none COC(=O)c1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 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: [50, 49, 19, 50, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 3, 5, 5, 50, 50, 50, 19, 19, 19, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 196) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347637366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347637366 none COC(=O)c1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 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: [50, 49, 19, 50, 19, 19, 19, 19, 19, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 19, 19, 19, 6, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347637366 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637366 Building ZINC000347637433 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347637433 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/197 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347637433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347637433 none CCOC(=O)c1cc(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 13, 40, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/198 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347637433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347637433 none CCOC(=O)c1cc(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 13, 39, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347637433 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 Building ZINC000347637433 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347637433 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 197) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1cc(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347637433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347637433 none CCOC(=O)c1cc(C)sc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 13, 40, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 198) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1cc(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347637433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347637433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347637433 none CCOC(=O)c1cc(C)sc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 5, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 13, 39, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 13, 13, 13, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347637433 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347637433 Building ZINC000347639925 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347639925 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/199 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Br)ccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347639925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347639925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347639925 none O=C(N1CCc2cc(Br)ccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/200 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2cc(Br)ccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347639925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347639925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347639925 none O=C(N1CCc2cc(Br)ccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 13 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347639925 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 Building ZINC000347639925 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347639925 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 199) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2cc(Br)ccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347639925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347639925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347639925 none O=C(N1CCc2cc(Br)ccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 200) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2cc(Br)ccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347639925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347639925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000347639925 none O=C(N1CCc2cc(Br)ccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 13 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347639925 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347639925 Building ZINC000347640793 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347640793 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/201 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1) `ZINC000347640793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347640793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347640793 none CN(C)c1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 35, 35, 35, 35, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/202 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1) `ZINC000347640793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347640793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347640793 none CN(C)c1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 49, 37, 37, 37, 37, 37, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 37, 37, 37, 37, 49, 49, 49, 49, 49, 49, 37, 37, 37, 6, 6, 6, 6, 6, 37, 37] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347640793 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 Building ZINC000347640793 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347640793 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 201) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)c1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1) `ZINC000347640793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347640793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347640793 none CN(C)c1ccc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 35, 35, 35, 35, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 202) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)c1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1) `ZINC000347640793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347640793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000347640793 none CN(C)c1ccc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 49, 37, 37, 37, 37, 37, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 37, 37, 37, 37, 49, 49, 49, 49, 49, 49, 37, 37, 37, 6, 6, 6, 6, 6, 37, 37] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347640793 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347640793 Building ZINC000347641507 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347641507 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/203 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347641507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347641507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347641507 none CC(C)(C)NC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 18, 49, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 4, 4, 4, 4, 4, 18] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/204 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347641507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347641507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347641507 none CC(C)(C)NC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 18, 49, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 4, 4, 4, 4, 4, 18] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347641507 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 Building ZINC000347641507 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347641507 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 203) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)NC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347641507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347641507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347641507 none CC(C)(C)NC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 18, 49, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 4, 4, 4, 4, 4, 18] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 204) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)NC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347641507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347641507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347641507 none CC(C)(C)NC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 18, 49, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 4, 4, 4, 4, 4, 18] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347641507 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347641507 Building ZINC000347663695 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347663695 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/205 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347663695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347663695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347663695 none CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 25, 25, 25, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 25, 45, 45, 45, 45, 25, 5, 5, 5, 5, 5, 25, 25] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/206 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347663695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347663695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347663695 none CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 23, 44, 44, 44, 44, 23, 5, 5, 5, 5, 5, 23, 23] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347663695 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 Building ZINC000347663695 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347663695 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 205) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347663695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347663695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347663695 none CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 25, 25, 25, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 25, 45, 45, 45, 45, 25, 5, 5, 5, 5, 5, 25, 25] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 206) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347663695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347663695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347663695 none CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 23, 44, 44, 44, 44, 23, 5, 5, 5, 5, 5, 23, 23] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347663695 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347663695 Building ZINC000347666419 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347666419 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/207 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347666419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666419 none O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 2, 2, 20, 29, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/208 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347666419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666419 none O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 2, 20, 32, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 5, 5, 30, 30, 50, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347666419 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 Building ZINC000347666419 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347666419 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 207) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347666419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666419 none O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 2, 2, 20, 29, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 208) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347666419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666419 none O=C(Nc1ccc(OC[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 2, 2, 20, 32, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 5, 5, 30, 30, 50, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347666419 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666419 Building ZINC000347666422 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347666422 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/209 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347666422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666422 none O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 4, 5, 23, 32, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 5, 5, 30, 30, 50, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/210 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347666422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666422 none O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 3, 4, 23, 30, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347666422 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 Building ZINC000347666422 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347666422 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 209) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347666422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666422 none O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 4, 5, 23, 32, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 5, 5, 30, 30, 50, 50, 50, 50, 50, 50, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 210) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347666422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347666422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000347666422 none O=C(Nc1ccc(OC[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 6, 6, 3, 4, 23, 30, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 6, 6, 29, 29, 50, 50, 50, 50, 50, 50, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347666422 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666422 Building ZINC000347666522 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347666522 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/211 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347666522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347666522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347666522 none CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 18, 18, 10, 18, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 10, 10, 2, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/212 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347666522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347666522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347666522 none CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 50, 50, 18, 18, 8, 18, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 11, 11, 2, 3, 3, 3, 3, 11, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347666522 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 Building ZINC000347666522 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347666522 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 211) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347666522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347666522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347666522 none CC(C)CNC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 18, 18, 10, 18, 7, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 10, 10, 2, 3, 3, 3, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 212) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347666522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347666522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347666522 none CC(C)CNC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 50, 50, 18, 18, 8, 18, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 11, 11, 2, 3, 3, 3, 3, 11, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347666522 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347666522 Building ZINC000347667798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347667798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/213 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347667798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347667798 none CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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: [5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 15, 50, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 50, 50, 50, 50, 50, 50, 15, 15, 5, 4, 4, 4, 4, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/214 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347667798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347667798 none CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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: [5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 50, 16, 16, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 50, 50, 50, 50, 50, 50, 16, 16, 6, 4, 4, 4, 4, 16] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347667798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 Building ZINC000347667798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347667798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 213) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347667798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347667798 none CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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: [5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 15, 50, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 50, 50, 50, 50, 50, 50, 15, 15, 5, 4, 4, 4, 4, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 214) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347667798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347667798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347667798 none CN(C)C(=O)c1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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: [5, 8, 5, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 50, 16, 16, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 16, 50, 50, 50, 50, 50, 50, 16, 16, 6, 4, 4, 4, 4, 16] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347667798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347667798 Building ZINC000347669193 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347669193 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/215 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(Oc2cnccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347669193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347669193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347669193 none O=C(Nc1cccc(Oc2cnccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/216 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(Oc2cnccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347669193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347669193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347669193 none O=C(Nc1cccc(Oc2cnccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347669193 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 Building ZINC000347669193 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347669193 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 215) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(Oc2cnccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347669193.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347669193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347669193 none O=C(Nc1cccc(Oc2cnccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 216) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(Oc2cnccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347669193.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347669193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347669193 none O=C(Nc1cccc(Oc2cnccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 8, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347669193 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347669193 Building ZINC000347672950 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347672950 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/217 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347672950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347672950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347672950 none CC(=O)Nc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 44, 44, 44, 44, 23, 23, 5, 5, 5, 5, 5, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/218 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347672950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347672950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347672950 none CC(=O)Nc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 43, 43, 43, 43, 23, 23, 5, 5, 5, 5, 5, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347672950 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 Building ZINC000347672950 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347672950 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 217) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(=O)Nc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347672950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347672950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347672950 none CC(=O)Nc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 44, 44, 44, 44, 23, 23, 5, 5, 5, 5, 5, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 218) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(=O)Nc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347672950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347672950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347672950 none CC(=O)Nc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 43, 43, 43, 43, 23, 23, 5, 5, 5, 5, 5, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347672950 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347672950 Building ZINC000347675011 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347675011 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/219 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347675011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347675011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347675011 none CCOCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 39, 25, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 49, 49, 46, 46, 25, 25, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/220 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347675011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347675011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347675011 none CCOCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 40, 24, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 49, 49, 47, 47, 24, 24, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347675011 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 Building ZINC000347675011 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347675011 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 219) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347675011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347675011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347675011 none CCOCCOCc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 39, 25, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 49, 49, 46, 46, 25, 25, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 220) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347675011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347675011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347675011 none CCOCCOCc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 40, 24, 6, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50, 49, 49, 47, 47, 24, 24, 2, 6, 6, 2, 2, 2, 2, 2, 6] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347675011 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675011 Building ZINC000347675014 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347675014 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/221 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347675014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675014 none CC[C@@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 45, 45, 27, 10, 27, 4, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 50, 50, 50, 50, 50, 45, 45, 45, 27, 17, 17, 3, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/222 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347675014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675014 none CC[C@@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 48, 48, 29, 12, 29, 12, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 29, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347675014 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 Building ZINC000347675014 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347675014 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 221) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347675014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675014 none CC[C@@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 45, 45, 27, 10, 27, 4, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 50, 50, 50, 50, 50, 45, 45, 45, 27, 17, 17, 3, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 222) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347675014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675014 none CC[C@@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 48, 48, 29, 12, 29, 12, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 48, 48, 48, 29, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347675014 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675014 Building ZINC000347675015 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347675015 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/223 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347675015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675015 none CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 49, 49, 29, 12, 29, 4, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 49, 49, 49, 29, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/224 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347675015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675015 none CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 45, 45, 27, 3, 27, 3, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 50, 50, 50, 50, 50, 45, 45, 45, 27, 17, 17, 3, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347675015 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 Building ZINC000347675015 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347675015 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 223) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347675015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675015 none CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 49, 49, 29, 12, 29, 4, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 49, 49, 49, 29, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 224) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000347675015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347675015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347675015 none CC[C@H](C)NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 45, 45, 27, 3, 27, 3, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 50, 50, 50, 50, 50, 45, 45, 45, 27, 17, 17, 3, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347675015 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347675015 Building ZINC000347678554 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347678554 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/225 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CCN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347678554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347678554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347678554 none O=C(Nc1ccc(CCN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 6, 6, 23, 34, 50, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 9, 9, 23, 23, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/226 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CCN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347678554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347678554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347678554 none O=C(Nc1ccc(CCN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 22, 33, 50, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 9, 9, 22, 22, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347678554 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 Building ZINC000347678554 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347678554 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 225) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(CCN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347678554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347678554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347678554 none O=C(Nc1ccc(CCN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 6, 6, 23, 34, 50, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 9, 9, 23, 23, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 226) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(CCN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347678554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347678554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347678554 none O=C(Nc1ccc(CCN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 22, 33, 50, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 9, 9, 22, 22, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347678554 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347678554 Building ZINC000347679099 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347679099 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/227 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347679099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347679099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347679099 none CN(C)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 50, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 5, 5, 5, 5, 5, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/228 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347679099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347679099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347679099 none CN(C)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 50, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 20, 20, 20, 48, 50, 50, 50, 50, 50, 20, 20, 5, 5, 5, 5, 5, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347679099 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 Building ZINC000347679099 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347679099 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 227) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347679099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347679099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347679099 none CN(C)C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 50, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 20, 5, 5, 5, 5, 5, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 228) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347679099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347679099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347679099 none CN(C)C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 50, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 20, 20, 20, 48, 50, 50, 50, 50, 50, 20, 20, 5, 5, 5, 5, 5, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347679099 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347679099 Building ZINC000347681483 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347681483 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/229 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347681483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347681483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347681483 none COc1ccc(OC(F)F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 30, 46, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 20, 20, 20, 15, 15, 46, 4, 3, 3, 3, 3, 15] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/230 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347681483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347681483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347681483 none COc1ccc(OC(F)F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 31, 47, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 20, 20, 20, 15, 15, 47, 4, 3, 3, 3, 3, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347681483 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 Building ZINC000347681483 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347681483 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 229) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(OC(F)F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347681483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347681483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347681483 none COc1ccc(OC(F)F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 30, 46, 46, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 20, 20, 20, 15, 15, 46, 4, 3, 3, 3, 3, 15] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 230) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(OC(F)F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347681483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347681483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347681483 none COc1ccc(OC(F)F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 31, 47, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 20, 20, 20, 15, 15, 47, 4, 3, 3, 3, 3, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347681483 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347681483 Building ZINC000347653718 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347653718 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/231 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC000347653718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347653718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347653718 none COc1cc(C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 12, 12, 25, 25, 25, 12, 12, 12, 12, 12, 4, 9, 12, 12, 9, 12, 12, 9, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/232 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC000347653718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347653718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347653718 none COc1cc(C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 12, 12, 24, 24, 24, 12, 12, 12, 12, 12, 4, 8, 13, 13, 8, 13, 13, 8, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347653718 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 Building ZINC000347653718 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347653718 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 231) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC000347653718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347653718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347653718 none COc1cc(C)cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 12, 12, 25, 25, 25, 12, 12, 12, 12, 12, 4, 9, 12, 12, 9, 12, 12, 9, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 232) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC000347653718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347653718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347653718 none COc1cc(C)cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 13, 13, 8, 12, 12, 24, 24, 24, 12, 12, 12, 12, 12, 4, 8, 13, 13, 8, 13, 13, 8, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347653718 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347653718 Building ZINC000347654128 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347654128 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/233 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)no1) `ZINC000347654128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347654128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347654128 none Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 4, 5, 5, 26, 46, 46, 46, 46, 46, 26, 26, 26, 5, 5, 5, 5, 5, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/234 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)no1) `ZINC000347654128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347654128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347654128 none Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 46, 46, 46, 46, 46, 26, 26, 26, 5, 5, 5, 5, 5, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347654128 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 Building ZINC000347654128 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347654128 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 233) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)no1) `ZINC000347654128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347654128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347654128 none Cc1nc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 4, 5, 5, 26, 46, 46, 46, 46, 46, 26, 26, 26, 5, 5, 5, 5, 5, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 234) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)no1) `ZINC000347654128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347654128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347654128 none Cc1nc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 46, 46, 46, 46, 46, 26, 26, 26, 5, 5, 5, 5, 5, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347654128 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347654128 Building ZINC000347658156 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347658156 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/235 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2csnn2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347658156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347658156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347658156 none O=C(Nc1ccc(c2csnn2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 17, 6, 6, 44, 48, 48, 44, 17, 17, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 17, 17, 42, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/236 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(c2csnn2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347658156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347658156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347658156 none O=C(Nc1ccc(c2csnn2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 18, 18, 7, 11, 50, 50, 50, 50, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 18, 18, 50, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347658156 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 Building ZINC000347658156 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347658156 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 235) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(c2csnn2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347658156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347658156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347658156 none O=C(Nc1ccc(c2csnn2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 17, 17, 6, 6, 44, 48, 48, 44, 17, 17, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 17, 17, 42, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 236) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(c2csnn2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347658156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347658156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347658156 none O=C(Nc1ccc(c2csnn2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 8, 8, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 18, 18, 7, 11, 50, 50, 50, 50, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 7, 18, 18, 50, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347658156 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347658156 Building ZINC000347697021 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347697021 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/237 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000347697021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347697021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000347697021 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 24, 24, 24, 24, 47, 24, 24, 47, 24, 6, 6, 6, 6, 6, 2, 2, 2, 2, 24, 24, 47, 47, 47, 47, 47, 47, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/238 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000347697021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347697021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000347697021 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 24, 24, 24, 24, 47, 24, 24, 47, 24, 6, 6, 6, 6, 6, 2, 2, 2, 2, 24, 24, 47, 47, 47, 47, 47, 47, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347697021 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 Building ZINC000347697021 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347697021 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 237) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000347697021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347697021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000347697021 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 24, 24, 24, 24, 47, 24, 24, 47, 24, 6, 6, 6, 6, 6, 2, 2, 2, 2, 24, 24, 47, 47, 47, 47, 47, 47, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 238) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000347697021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347697021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000347697021 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 24, 24, 24, 24, 47, 24, 24, 47, 24, 6, 6, 6, 6, 6, 2, 2, 2, 2, 24, 24, 47, 47, 47, 47, 47, 47, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347697021 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697021 Building ZINC000347697144 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347697144 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/239 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347697144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347697144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347697144 none Cc1nccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/240 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347697144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347697144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347697144 none Cc1nccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347697144 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 Building ZINC000347697144 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347697144 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 239) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347697144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347697144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347697144 none Cc1nccc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 240) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347697144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347697144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347697144 none Cc1nccc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347697144 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347697144 Building ZINC000347682412 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347682412 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/241 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347682412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347682412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347682412 none CC(C)C(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 28, 28, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 50, 50, 50, 50, 50, 50, 50, 28, 16, 16, 16, 3, 3, 3, 3, 3, 16] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/242 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347682412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347682412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347682412 none CC(C)C(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 28, 28, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 2, 3, 3, 16, 50, 50, 50, 50, 50, 50, 50, 28, 16, 16, 16, 3, 3, 3, 3, 3, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347682412 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 Building ZINC000347682412 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347682412 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 241) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)C(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347682412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347682412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347682412 none CC(C)C(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 28, 28, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 50, 50, 50, 50, 50, 50, 50, 28, 16, 16, 16, 3, 3, 3, 3, 3, 16] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 242) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)C(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347682412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347682412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347682412 none CC(C)C(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 28, 28, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 2, 3, 3, 16, 50, 50, 50, 50, 50, 50, 50, 28, 16, 16, 16, 3, 3, 3, 3, 3, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347682412 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682412 Building ZINC000347682474 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347682474 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/243 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1) `ZINC000347682474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347682474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347682474 none Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 28, 15, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/244 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1) `ZINC000347682474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347682474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347682474 none Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 28, 14, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347682474 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 Building ZINC000347682474 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347682474 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 243) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1) `ZINC000347682474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347682474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347682474 none Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 28, 15, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 244) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1) `ZINC000347682474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347682474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347682474 none Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'F', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 28, 14, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 4, 3, 3, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347682474 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347682474 Building ZINC000347683545 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347683545 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/245 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347683545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347683545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347683545 none CCN(CC)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 44, 49, 11, 11, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 11, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 41, 41, 2, 11, 11, 2, 3, 3, 3, 3, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 233 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/246 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347683545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347683545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347683545 none CCN(CC)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 44, 49, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 40, 40, 3, 11, 11, 3, 3, 3, 3, 3, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347683545 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 Building ZINC000347683545 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347683545 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 245) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(CC)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347683545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347683545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347683545 none CCN(CC)Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 44, 49, 11, 11, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 11, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 41, 41, 2, 11, 11, 2, 3, 3, 3, 3, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 233 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 246) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(CC)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347683545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347683545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347683545 none CCN(CC)Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 40, 44, 49, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 40, 40, 3, 11, 11, 3, 3, 3, 3, 3, 11] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347683545 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683545 Building ZINC000347683717 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347683717 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/247 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347683717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347683717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347683717 none Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 4, 39, 39, 39, 50, 50, 17, 17, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 39, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/248 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347683717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347683717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347683717 none Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 7, 39, 39, 39, 50, 50, 17, 17, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 39, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347683717 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 Building ZINC000347683717 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347683717 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 247) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347683717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347683717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347683717 none Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 4, 39, 39, 39, 50, 50, 17, 17, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 39, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 248) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347683717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347683717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347683717 none Cc1cc(C(=O)NC(C)C)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 7, 39, 39, 39, 50, 50, 17, 17, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 39, 50, 50, 50, 50, 50, 50, 50, 17, 17, 4, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347683717 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347683717 Building ZINC000347685793 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347685793 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/249 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)Cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1) `ZINC000347685793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347685793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347685793 none CC1(C)Cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 17, 17, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 6, 6, 6, 34, 34] 48 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/250 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)Cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1) `ZINC000347685793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347685793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347685793 none CC1(C)Cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 17, 17, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 6, 6, 6, 34, 34] 48 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347685793 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 Building ZINC000347685793 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347685793 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 249) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC1(C)Cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1) `ZINC000347685793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347685793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347685793 none CC1(C)Cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 17, 17, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 6, 6, 6, 34, 34] 48 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 250) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC1(C)Cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1) `ZINC000347685793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347685793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000347685793 none CC1(C)Cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc2C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 17, 17, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 6, 6, 6, 6, 34, 34] 48 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347685793 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347685793 Building ZINC000347687618 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347687618 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/251 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2CCCCC2=O)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347687618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347687618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347687618 none O=C(Nc1cccc(N2CCCCC2=O)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 19, 19, 19, 23, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/252 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2CCCCC2=O)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347687618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347687618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347687618 none O=C(Nc1cccc(N2CCCCC2=O)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 18, 18, 18, 22, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347687618 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 Building ZINC000347687618 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347687618 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 251) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2CCCCC2=O)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347687618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347687618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347687618 none O=C(Nc1cccc(N2CCCCC2=O)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 19, 19, 19, 23, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 19, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 252) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(N2CCCCC2=O)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347687618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347687618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347687618 none O=C(Nc1cccc(N2CCCCC2=O)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 18, 18, 18, 22, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347687618 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687618 Building ZINC000347687669 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347687669 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/253 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)c2)cn1) `ZINC000347687669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347687669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347687669 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)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.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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, 1, 1, 1, 1, 3, 3, 4, 12, 16, 16, 16, 16, 4, 19, 19, 12, 19, 19, 19, 5, 5, 5, 5, 5, 5, 12, 12, 16, 16, 16, 19, 19, 19, 19, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/254 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)c2)cn1) `ZINC000347687669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347687669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347687669 none Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)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.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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, 1, 1, 1, 1, 3, 3, 4, 12, 16, 16, 16, 16, 4, 20, 20, 11, 20, 20, 20, 5, 5, 5, 5, 5, 5, 12, 12, 16, 16, 16, 20, 20, 20, 20, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347687669 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 Building ZINC000347687669 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347687669 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 253) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)c2)cn1) `ZINC000347687669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347687669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347687669 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)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.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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, 1, 1, 1, 1, 3, 3, 4, 12, 16, 16, 16, 16, 4, 19, 19, 12, 19, 19, 19, 5, 5, 5, 5, 5, 5, 12, 12, 16, 16, 16, 19, 19, 19, 19, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 254) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)c2)cn1) `ZINC000347687669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347687669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347687669 none Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccco2)c2cccc(Cl)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.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 8, 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, 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, 1, 1, 1, 1, 3, 3, 4, 12, 16, 16, 16, 16, 4, 20, 20, 11, 20, 20, 20, 5, 5, 5, 5, 5, 5, 12, 12, 16, 16, 16, 20, 20, 20, 20, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347687669 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687669 Building ZINC000347687725 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347687725 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/255 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347687725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347687725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347687725 none Cc1cc(C)n(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/256 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347687725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347687725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347687725 none Cc1cc(C)n(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347687725 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 Building ZINC000347687725 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347687725 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 255) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(C)n(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347687725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347687725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347687725 none Cc1cc(C)n(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 256) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(C)n(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347687725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347687725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347687725 none Cc1cc(C)n(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 17, 17, 17, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 3, 3, 3, 3, 3, 17] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347687725 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347687725 Building ZINC000347692703 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347692703 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/257 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O) `ZINC000347692703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347692703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347692703 none CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 41, 29, 11, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 41, 49, 49, 42, 42, 42, 42, 42, 29, 29, 11, 3, 11, 11, 3, 3, 3, 3, 3, 49, 49, 49] 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: 200 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/258 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O) `ZINC000347692703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347692703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347692703 none CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 30, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 41, 50, 50, 41, 41, 41, 41, 41, 30, 30, 12, 12, 12, 12, 3, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347692703 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 Building ZINC000347692703 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347692703 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 257) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O) `ZINC000347692703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347692703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347692703 none CCN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 41, 29, 11, 11, 11, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 41, 49, 49, 42, 42, 42, 42, 42, 29, 29, 11, 3, 11, 11, 3, 3, 3, 3, 3, 49, 49, 49] 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: 200 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 258) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O) `ZINC000347692703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347692703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347692703 none CCN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 30, 12, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 41, 50, 50, 41, 41, 41, 41, 41, 30, 30, 12, 12, 12, 12, 3, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347692703 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347692703 Building ZINC000347695567 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347695567 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/259 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347695567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347695567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347695567 none O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 49, 49, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/260 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347695567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347695567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347695567 none O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 49, 49, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347695567 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 Building ZINC000347695567 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347695567 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 259) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347695567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347695567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347695567 none O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 49, 49, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 260) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347695567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347695567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347695567 none O=C(Nc1ccnn1Cc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 49, 49, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347695567 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695567 Building ZINC000347695659 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347695659 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/261 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)o1) `ZINC000347695659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347695659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347695659 none Cc1nnc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 50, 50, 50, 50, 18, 18, 18, 18, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/262 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)o1) `ZINC000347695659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347695659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347695659 none Cc1nnc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 18, 18, 18, 17, 18, 18, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 50, 18, 18, 18, 18, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347695659 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 Building ZINC000347695659 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347695659 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 261) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nnc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)o1) `ZINC000347695659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347695659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347695659 none Cc1nnc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 50, 50, 50, 50, 18, 18, 18, 18, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 262) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nnc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)o1) `ZINC000347695659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347695659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000347695659 none Cc1nnc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 18, 18, 18, 17, 18, 18, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 50, 18, 18, 18, 18, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347695659 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347695659 Building ZINC000347696584 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347696584 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/263 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347696584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347696584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347696584 none Cc1cc(C)n(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/264 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347696584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347696584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347696584 none Cc1cc(C)n(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 3, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347696584 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 Building ZINC000347696584 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347696584 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 263) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(C)n(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347696584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347696584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347696584 none Cc1cc(C)n(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 264) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(C)n(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC000347696584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347696584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347696584 none Cc1cc(C)n(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.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, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 3, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 6, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347696584 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347696584 Building ZINC000347706298 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347706298 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/265 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347706298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347706298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347706298 none Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 23, 23, 23, 50, 50, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 23, 50, 50, 50, 50, 50, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/266 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347706298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347706298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347706298 none Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 24, 24, 24, 50, 50, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 24, 50, 50, 50, 50, 50, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347706298 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 Building ZINC000347706298 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347706298 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 265) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347706298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347706298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347706298 none Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 23, 23, 23, 50, 50, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 23, 50, 50, 50, 50, 50, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 266) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347706298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347706298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347706298 none Cc1ccc(NC(=O)C2CC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 24, 24, 24, 50, 50, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 13, 24, 50, 50, 50, 50, 50, 13, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347706298 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706298 Building ZINC000347706445 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347706445 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/267 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1) `ZINC000347706445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347706445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347706445 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 26, 26, 50, 50, 29, 50, 50, 50, 26, 26, 26, 26, 26, 9, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/268 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1) `ZINC000347706445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347706445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347706445 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 50, 50, 29, 50, 50, 50, 25, 25, 25, 25, 25, 9, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347706445 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 Building ZINC000347706445 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347706445 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 267) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1) `ZINC000347706445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347706445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347706445 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 26, 26, 50, 50, 29, 50, 50, 50, 26, 26, 26, 26, 26, 9, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 268) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1) `ZINC000347706445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347706445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347706445 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n(c2ccccc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 25, 25, 50, 50, 29, 50, 50, 50, 25, 25, 25, 25, 25, 9, 3, 3, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347706445 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706445 Building ZINC000347706482 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347706482 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/269 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347706482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347706482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347706482 none Cc1cccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 26, 11, 11, 11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 45, 50, 50, 26, 26, 11, 11, 5, 2, 2, 2, 2, 50] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/270 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347706482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347706482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347706482 none Cc1cccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 26, 11, 11, 11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 45, 50, 50, 26, 26, 11, 11, 5, 2, 2, 2, 2, 50] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347706482 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 Building ZINC000347706482 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347706482 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 269) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347706482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347706482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347706482 none Cc1cccc(Cn2nccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 26, 11, 11, 11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 45, 50, 50, 26, 26, 11, 11, 5, 2, 2, 2, 2, 50] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 270) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347706482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347706482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347706482 none Cc1cccc(Cn2nccc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 26, 11, 11, 11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 45, 50, 50, 26, 26, 11, 11, 5, 2, 2, 2, 2, 50] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347706482 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347706482 Building ZINC000347710503 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347710503 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/271 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)Nc1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347710503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347710503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347710503 none CCC(=O)Nc1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 25, 26, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 26, 14, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/272 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)Nc1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347710503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347710503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347710503 none CCC(=O)Nc1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 25, 26, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 26, 14, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347710503 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 Building ZINC000347710503 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347710503 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 271) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCC(=O)Nc1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347710503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347710503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347710503 none CCC(=O)Nc1ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 25, 26, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 26, 14, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 272) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCC(=O)Nc1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347710503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347710503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347710503 none CCC(=O)Nc1ccc(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 25, 26, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 50, 50, 50, 50, 50, 26, 14, 14, 14, 14, 14, 4, 3, 3, 3, 3, 14] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347710503 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347710503 Building ZINC000347713705 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347713705 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/273 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347713705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347713705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347713705 none O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 20, 22, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 22, 22, 50, 50, 50, 22, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/274 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347713705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347713705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347713705 none O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 23, 23, 20, 23, 50, 50, 50, 50, 23, 23, 23, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 23, 23, 50, 50, 50, 23, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347713705 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 Building ZINC000347713705 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347713705 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 273) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347713705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347713705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347713705 none O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 22, 22, 20, 22, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 22, 22, 50, 50, 50, 22, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 274) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347713705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347713705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347713705 none O=C(Nc1ccc(n2cccn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 23, 23, 20, 23, 50, 50, 50, 50, 23, 23, 23, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 23, 23, 50, 50, 50, 23, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347713705 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347713705 Building ZINC000347714479 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347714479 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/275 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2) `ZINC000347714479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347714479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347714479 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/276 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2) `ZINC000347714479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347714479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347714479 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347714479 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 Building ZINC000347714479 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347714479 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 275) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2) `ZINC000347714479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347714479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347714479 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 276) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2) `ZINC000347714479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347714479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000347714479 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(C)(C)c1ccc2c(c1)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347714479 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347714479 Building ZINC000347699396 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347699396 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/277 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/278 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/279 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/279' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/280 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/280' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699396 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 Building ZINC000347699396 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347699396 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 277) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 278) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 279) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 280) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699396 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 Building ZINC000347699396 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347699396 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 277) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 278) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 279) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 280) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699396 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 Building ZINC000347699396 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347699396 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 277) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 278) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 25, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 279) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 280) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1) `ZINC000347699396.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347699396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000347699396 none CCCN1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 30, 30, 30, 30, 30, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 50, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 24, 3, 3, 3, 3, 3, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699396 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699396 Building ZINC000347699520 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347699520 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/281 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21) `ZINC000347699520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347699520 none Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 6, 6, 6, 6, 11, 11, 11] 11 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/282 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21) `ZINC000347699520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347699520 none Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 6, 6, 6, 6, 11, 11, 11] 11 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699520 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 Building ZINC000347699520 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347699520 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 281) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21) `ZINC000347699520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347699520 none Cn1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 6, 6, 6, 6, 11, 11, 11] 11 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 282) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21) `ZINC000347699520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347699520 none Cn1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 6, 6, 6, 6, 11, 11, 11] 11 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699520 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699520 Building ZINC000347699986 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347699986 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/283 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347699986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347699986 none CN(C)C(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 50, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 4, 3, 3, 3, 3, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/284 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347699986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347699986 none CN(C)C(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 50, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 4, 3, 3, 3, 3, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699986 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 Building ZINC000347699986 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347699986 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 283) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)C(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347699986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347699986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347699986 none CN(C)C(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 50, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 4, 3, 3, 3, 3, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 284) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)C(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl) `ZINC000347699986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347699986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347699986 none CN(C)C(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 50, 21, 21, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 4, 3, 3, 3, 3, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347699986 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347699986 Building ZINC000347700354 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347700354 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/285 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347700354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347700354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347700354 none O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 26, 26, 18, 26, 50, 50, 50, 50, 26, 26, 26, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 26, 26, 50, 50, 50, 26, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/286 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347700354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347700354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347700354 none O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 26, 26, 18, 26, 50, 50, 50, 50, 26, 26, 26, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 26, 26, 50, 50, 50, 26, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347700354 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 Building ZINC000347700354 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347700354 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 285) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347700354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347700354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347700354 none O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 26, 26, 18, 26, 50, 50, 50, 50, 26, 26, 26, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 26, 26, 50, 50, 50, 26, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 286) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347700354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347700354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347700354 none O=C(Nc1ccc(n2ccnc2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 26, 26, 18, 26, 50, 50, 50, 50, 26, 26, 26, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 26, 26, 50, 50, 50, 26, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347700354 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347700354 Building ZINC000347703827 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347703827 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/287 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)OCCO2) `ZINC000347703827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347703827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347703827 none CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 19, 26, 26, 26, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 3, 5, 5, 26, 26, 26, 26, 50, 50, 50, 26, 26, 6, 5, 5, 5, 5, 26, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/288 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)OCCO2) `ZINC000347703827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347703827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347703827 none CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 27, 27, 27, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 50, 50, 50, 27, 27, 6, 5, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347703827 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 Building ZINC000347703827 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347703827 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 287) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)OCCO2) `ZINC000347703827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347703827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347703827 none CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 19, 26, 26, 26, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 3, 5, 5, 26, 26, 26, 26, 50, 50, 50, 26, 26, 6, 5, 5, 5, 5, 26, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 288) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)OCCO2) `ZINC000347703827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347703827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347703827 none CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 27, 27, 27, 19, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 27, 50, 50, 50, 27, 27, 6, 5, 5, 5, 5, 27, 27, 27, 27] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347703827 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347703827 Building ZINC000347705364 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347705364 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/289 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1CCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347705364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347705364 none O=C(Nc1ccnn1CCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/290 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1CCc1ccccc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347705364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347705364 none O=C(Nc1ccnn1CCc1ccccc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347705364 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 Building ZINC000347705364 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347705364 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 289) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1CCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347705364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347705364 none O=C(Nc1ccnn1CCc1ccccc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 290) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1CCc1ccccc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347705364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347705364 none O=C(Nc1ccnn1CCc1ccccc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347705364 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705364 Building ZINC000347705993 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347705993 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/291 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347705993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347705993 none O=C(Nc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 14, 28, 28, 28, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/292 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347705993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347705993 none O=C(Nc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 17, 24, 24, 24, 49, 49, 49, 49, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 24, 24, 24, 49, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347705993 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 Building ZINC000347705993 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347705993 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 291) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347705993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347705993 none O=C(Nc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 14, 28, 28, 28, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 292) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347705993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347705993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347705993 none O=C(Nc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 24, 24, 24, 17, 24, 24, 24, 49, 49, 49, 49, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 24, 24, 24, 49, 49, 49, 49, 49, 49, 49, 49, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347705993 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347705993 Building ZINC000347738911 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347738911 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/293 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347738911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347738911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347738911 none O=C(Nc1ccnn1c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 46, 1, 1, 1, 4, 4, 1, 2, 4, 4, 9, 24, 24, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/294 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347738911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347738911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347738911 none O=C(Nc1ccnn1c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 46, 1, 1, 1, 4, 4, 1, 1, 4, 4, 9, 24, 24, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347738911 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 Building ZINC000347738911 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347738911 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 293) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347738911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347738911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347738911 none O=C(Nc1ccnn1c1cccc(Cl)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 46, 1, 1, 1, 4, 4, 1, 2, 4, 4, 9, 24, 24, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 110 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 294) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347738911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347738911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347738911 none O=C(Nc1ccnn1c1cccc(Cl)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 46, 1, 1, 1, 4, 4, 1, 1, 4, 4, 9, 24, 24, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347738911 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347738911 Building ZINC000347739056 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347739056 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/295 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347739056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347739056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347739056 none CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 22, 22, 22, 8, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 46, 22, 22, 22, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/296 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347739056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347739056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347739056 none CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 21, 21, 21, 14, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 46, 21, 21, 21, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347739056 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 Building ZINC000347739056 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347739056 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 295) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347739056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347739056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347739056 none CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 22, 22, 22, 8, 22, 22, 22, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 46, 22, 22, 22, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 296) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347739056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347739056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347739056 none CC(=O)Nc1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 21, 21, 21, 14, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 46, 21, 21, 21, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347739056 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347739056 Building ZINC000347717673 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347717673 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/297 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC2CCCC2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347717673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347717673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347717673 none O=C(Nc1ccc(OC2CCCC2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 39, 50, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/298 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC2CCCC2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347717673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347717673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347717673 none O=C(Nc1ccc(OC2CCCC2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 38, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347717673 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 Building ZINC000347717673 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347717673 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 297) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC2CCCC2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347717673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347717673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347717673 none O=C(Nc1ccc(OC2CCCC2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 9, 9, 39, 50, 50, 50, 50, 9, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 298) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC2CCCC2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347717673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347717673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347717673 none O=C(Nc1ccc(OC2CCCC2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 10, 10, 38, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347717673 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347717673 Building ZINC000347726759 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347726759 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/299 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347726759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726759 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 27, 27, 5, 4, 4, 4, 4, 38, 38, 38, 38] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/300 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347726759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726759 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 24, 24, 6, 4, 4, 4, 4, 42, 42, 42, 42] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347726759 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 Building ZINC000347726759 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347726759 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 299) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347726759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726759 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 27, 27, 5, 4, 4, 4, 4, 38, 38, 38, 38] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 300) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347726759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726759 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 24, 24, 6, 4, 4, 4, 4, 42, 42, 42, 42] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347726759 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726759 Building ZINC000347726761 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347726761 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/301 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347726761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726761 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 2, 2, 4, 4, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 24, 24, 6, 4, 4, 4, 4, 42, 42, 42, 42] 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/302 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347726761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726761 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 27, 27, 5, 4, 4, 4, 4, 38, 38, 38, 38] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347726761 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 Building ZINC000347726761 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347726761 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 301) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347726761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726761 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 2, 2, 4, 4, 12, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 24, 24, 24, 6, 4, 4, 4, 4, 42, 42, 42, 42] 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: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 302) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1) `ZINC000347726761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347726761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347726761 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1nc2ccccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 27, 27, 27, 5, 4, 4, 4, 4, 38, 38, 38, 38] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347726761 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347726761 Building ZINC000347788616 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347788616 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/303 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347788616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788616 none O=C(NC[C@@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 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, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/304 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347788616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788616 none O=C(NC[C@@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 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, 37, 38]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347788616 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 Building ZINC000347788616 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347788616 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 303) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(NC[C@@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347788616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788616 none O=C(NC[C@@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 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, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 304) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(NC[C@@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347788616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788616 none O=C(NC[C@@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 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, 37, 38]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347788616 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788616 Building ZINC000347788619 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347788619 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/305 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347788619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788619 none O=C(NC[C@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 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, 37, 38]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/306 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347788619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788619 none O=C(NC[C@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 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, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347788619 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 Building ZINC000347788619 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347788619 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 305) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(NC[C@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347788619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788619 none O=C(NC[C@H]1SCCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 17, 17, 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, 37, 38]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 306) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(NC[C@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347788619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347788619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347788619 none O=C(NC[C@H]1SCCc2ccccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 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, 37, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347788619 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347788619 Building ZINC000347798640 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798640 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/307 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/308 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/309 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/309' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/310 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/310' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798640 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 Building ZINC000347798640 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798640 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 307) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 308) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 309) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 310) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798640 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 Building ZINC000347798640 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798640 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 307) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 308) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 309) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 310) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798640 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 Building ZINC000347798640 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798640 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 307) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 308) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 48, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 309) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 310) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798640.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798640 none O=C(N[C@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 47, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798640 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798640 Building ZINC000347798643 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798643 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/311 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/312 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/313 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/313' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/314 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/314' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798643 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 Building ZINC000347798643 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798643 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 311) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 312) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 313) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 314) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798643 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 Building ZINC000347798643 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798643 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 311) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 312) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 313) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 314) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798643 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 Building ZINC000347798643 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347798643 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 311) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 312) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 21, 50, 50, 45, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 313) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 314) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCN(c2cccc(Cl)c2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347798643.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347798643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347798643 none O=C(N[C@@H]1CCN(c2cccc(Cl)c2)C1)[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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 5, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347798643 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347798643 Building ZINC000347823940 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823940 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/315 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000347823940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823940 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 19, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 19, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/316 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000347823940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823940 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 21, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 5, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823940 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 Building ZINC000347823940 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823940 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 315) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000347823940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823940 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 19, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 19, 19, 19, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 316) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C) `ZINC000347823940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823940 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 21, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 5, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823940 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823940 Building ZINC000347823953 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823953 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/317 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823953 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 21, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/318 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823953 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 6, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823953 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 Building ZINC000347823953 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823953 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 317) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823953 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 34, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 21, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 318) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823953 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 6, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823953 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823953 Building ZINC000347823977 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823977 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/319 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823977 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 6, 1, 6, 1, 1, 1, 4, 4, 1, 2, 4, 4, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 6, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/320 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823977 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 156 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823977 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 Building ZINC000347823977 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823977 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 319) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823977 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 6, 1, 6, 1, 1, 1, 4, 4, 1, 2, 4, 4, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 6, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 320) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C) `ZINC000347823977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823977 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 18, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 6, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 156 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823977 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823977 Building ZINC000347823991 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823991 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/321 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000347823991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823991 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 24, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 6, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/322 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000347823991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823991 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 24, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 24, 24, 24, 6, 5, 5, 5, 5, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823991 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 Building ZINC000347823991 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347823991 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 321) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000347823991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347823991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823991 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 24, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 6, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 158 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 322) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C) `ZINC000347823991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347823991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347823991 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)[C@H]1Oc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 24, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 24, 24, 24, 6, 5, 5, 5, 5, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347823991 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347823991 Building ZINC000347830786 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347830786 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/323 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ncc[nH]1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347830786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347830786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347830786 none O=C(N(Cc1ncc[nH]1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 18, 21, 21, 21, 21, 21, 8, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 18, 21, 21, 32, 32, 32, 32, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/324 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ncc[nH]1)c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347830786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347830786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347830786 none O=C(N(Cc1ncc[nH]1)c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 18, 20, 20, 20, 20, 20, 8, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 20, 20, 34, 34, 34, 34, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347830786 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 Building ZINC000347830786 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347830786 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 323) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(Cc1ncc[nH]1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347830786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347830786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347830786 none O=C(N(Cc1ncc[nH]1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 18, 21, 21, 21, 21, 21, 8, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 18, 21, 21, 32, 32, 32, 32, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 324) grep: /scratch/xiaobo/318708/xbg-8058115.33/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(Cc1ncc[nH]1)c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347830786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347830786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347830786 none O=C(N(Cc1ncc[nH]1)c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 18, 20, 20, 20, 20, 20, 8, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 20, 20, 34, 34, 34, 34, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347830786 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347830786 Building ZINC000347831388 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347831388 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/325 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347831388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347831388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347831388 none COCCCOc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 23, 20, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 50, 50, 50, 50, 50, 43, 43, 23, 23, 7, 7, 7, 2, 2, 2, 2, 2, 7] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/326 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347831388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347831388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347831388 none COCCCOc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 21, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 50, 50, 50, 50, 50, 45, 45, 25, 25, 8, 8, 8, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347831388 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 Building ZINC000347831388 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347831388 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 325) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCCOc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347831388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347831388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347831388 none COCCCOc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 23, 20, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 50, 50, 50, 50, 50, 43, 43, 23, 23, 7, 7, 7, 2, 2, 2, 2, 2, 7] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 326) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCCOc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347831388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347831388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347831388 none COCCCOc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 21, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 50, 50, 50, 50, 50, 45, 45, 25, 25, 8, 8, 8, 2, 2, 2, 2, 2, 8] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347831388 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347831388 Building ZINC000347832051 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347832051 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/327 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br) `ZINC000347832051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347832051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347832051 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 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: [16, 16, 16, 9, 9, 1, 9, 1, 1, 1, 5, 5, 2, 2, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 9, 5, 5, 5, 5, 16] 18 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/328 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br) `ZINC000347832051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347832051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347832051 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 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: [16, 16, 16, 9, 9, 1, 9, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 9, 5, 5, 5, 5, 16] 18 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347832051 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 Building ZINC000347832051 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347832051 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 327) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br) `ZINC000347832051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347832051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347832051 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 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: [16, 16, 16, 9, 9, 1, 9, 1, 1, 1, 5, 5, 2, 2, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 9, 5, 5, 5, 5, 16] 18 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 328) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br) `ZINC000347832051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347832051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347832051 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ncc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 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: [16, 16, 16, 9, 9, 1, 9, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 9, 5, 5, 5, 5, 16] 18 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347832051 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832051 Building ZINC000347832148 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347832148 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/329 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347832148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832148 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 11, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 34, 50, 50, 50, 50, 50, 50, 25, 25, 25, 24, 25, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/330 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347832148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832148 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 36, 50, 50, 50, 50, 50, 50, 24, 24, 24, 23, 24, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347832148 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 Building ZINC000347832148 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347832148 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 329) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347832148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832148 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 11, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 34, 50, 50, 50, 50, 50, 50, 25, 25, 25, 24, 25, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 330) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347832148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832148 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 36, 50, 50, 50, 50, 50, 50, 24, 24, 24, 23, 24, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347832148 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832148 Building ZINC000347832149 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347832149 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/331 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347832149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832149 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 36, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 23, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/332 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347832149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832149 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 11, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 34, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 24, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347832149 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 Building ZINC000347832149 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347832149 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 331) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347832149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832149 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 36, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 23, 10, 10, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 332) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1) `ZINC000347832149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347832149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347832149 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 11, 19, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 19, 34, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 24, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347832149 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347832149 Building ZINC000347834612 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347834612 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/333 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1) `ZINC000347834612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347834612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347834612 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 10, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 10, 10, 10, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/334 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1) `ZINC000347834612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347834612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347834612 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 26, 26, 26, 26, 50, 50, 47, 50, 50, 26, 26, 10, 10, 10, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347834612 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 Building ZINC000347834612 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347834612 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 333) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1) `ZINC000347834612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347834612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347834612 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 10, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 10, 10, 10, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 334) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1) `ZINC000347834612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347834612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000347834612 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(c2ccccc2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.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, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 26, 26, 26, 26, 50, 50, 47, 50, 50, 26, 26, 10, 10, 10, 2, 2, 2, 2, 26, 26, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347834612 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347834612 Building ZINC000347837045 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347837045 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/335 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C2CC2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347837045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347837045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347837045 none COC(=O)c1c(C2CC2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 44, 11, 11, 11, 31, 31, 11, 11, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 44, 44, 44, 31, 31, 31, 31, 31, 11, 4, 4, 4, 4, 4] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/336 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C2CC2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347837045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347837045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347837045 none COC(=O)c1c(C2CC2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 12, 41, 12, 12, 12, 34, 34, 12, 12, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 41, 41, 41, 34, 34, 34, 34, 34, 12, 4, 4, 4, 4, 4] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347837045 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 Building ZINC000347837045 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347837045 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 335) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2CC2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347837045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347837045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347837045 none COC(=O)c1c(C2CC2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 44, 11, 11, 11, 31, 31, 11, 11, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 44, 44, 44, 31, 31, 31, 31, 31, 11, 4, 4, 4, 4, 4] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 336) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2CC2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347837045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347837045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347837045 none COC(=O)c1c(C2CC2)csc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 5, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 12, 41, 12, 12, 12, 34, 34, 12, 12, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 41, 41, 41, 34, 34, 34, 34, 34, 12, 4, 4, 4, 4, 4] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347837045 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347837045 Building ZINC000347838495 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347838495 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/337 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1) `ZINC000347838495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347838495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347838495 none Cc1csc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 13, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/338 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1) `ZINC000347838495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347838495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347838495 none Cc1csc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 22, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347838495 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 Building ZINC000347838495 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347838495 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 337) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1csc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1) `ZINC000347838495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347838495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347838495 none Cc1csc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 13, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 25, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 338) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1csc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1) `ZINC000347838495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347838495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347838495 none Cc1csc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)CCCC2)n1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 22, 50, 50, 50, 50, 50, 5, 3, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347838495 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347838495 Building ZINC000347841596 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347841596 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/339 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1) `ZINC000347841596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347841596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347841596 none Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 27, 33, 50, 50, 20, 20, 20, 20, 20, 20, 9, 9, 2, 2, 2, 2, 2, 33, 33, 50, 50, 50, 50, 50, 20] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/340 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1) `ZINC000347841596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347841596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347841596 none Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 21, 20, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 21, 31, 37, 50, 50, 21, 21, 21, 21, 21, 21, 10, 10, 2, 2, 2, 2, 2, 37, 37, 50, 50, 50, 50, 50, 21] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347841596 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 Building ZINC000347841596 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347841596 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 339) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1) `ZINC000347841596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347841596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347841596 none Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 27, 33, 50, 50, 20, 20, 20, 20, 20, 20, 9, 9, 2, 2, 2, 2, 2, 33, 33, 50, 50, 50, 50, 50, 20] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 340) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1) `ZINC000347841596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347841596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347841596 none Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(OCC2CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 21, 20, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 21, 31, 37, 50, 50, 21, 21, 21, 21, 21, 21, 10, 10, 2, 2, 2, 2, 2, 37, 37, 50, 50, 50, 50, 50, 21] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347841596 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841596 Building ZINC000347841974 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347841974 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/341 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347841974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841974 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 45, 45, 45, 45, 45, 50, 50, 50, 50, 45, 7, 7, 7, 4, 3, 3, 3, 3, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/342 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347841974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841974 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 45, 45, 45, 45, 45, 50, 50, 50, 50, 45, 8, 8, 8, 4, 3, 3, 3, 3, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347841974 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 Building ZINC000347841974 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347841974 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 341) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347841974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841974 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 45, 45, 45, 45, 45, 50, 50, 50, 50, 45, 7, 7, 7, 4, 3, 3, 3, 3, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 342) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347841974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841974 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 45, 45, 45, 45, 45, 50, 50, 50, 50, 45, 8, 8, 8, 4, 3, 3, 3, 3, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 95 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347841974 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841974 Building ZINC000347841975 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347841975 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/343 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347841975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841975 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 48, 48, 48, 48, 48, 50, 50, 50, 50, 48, 8, 8, 8, 4, 3, 3, 3, 3, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 48] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/344 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347841975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841975 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 45, 45, 45, 45, 45, 50, 50, 50, 50, 45, 7, 7, 7, 4, 3, 3, 3, 3, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347841975 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 Building ZINC000347841975 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347841975 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 343) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347841975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841975 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 48, 48, 48, 48, 48, 50, 50, 50, 50, 48, 8, 8, 8, 4, 3, 3, 3, 3, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 48] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 344) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1) `ZINC000347841975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347841975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347841975 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 45, 45, 45, 45, 45, 50, 50, 50, 50, 45, 7, 7, 7, 4, 3, 3, 3, 3, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 89 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347841975 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347841975 Building ZINC000347843162 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347843162 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/345 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C) `ZINC000347843162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347843162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347843162 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 48, 48, 48, 50, 50, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 18, 48, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/346 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C) `ZINC000347843162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347843162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347843162 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 47, 47, 47, 50, 50, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 47, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347843162 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 Building ZINC000347843162 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347843162 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 345) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C) `ZINC000347843162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347843162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347843162 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 48, 48, 48, 50, 50, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 18, 48, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 346) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C) `ZINC000347843162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347843162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347843162 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 47, 47, 47, 50, 50, 17, 17, 17, 17, 17, 4, 3, 3, 3, 3, 17, 47, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347843162 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347843162 Building ZINC000347849840 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347849840 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/347 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347849840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849840 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 35, 50, 50, 36, 50, 50, 50, 26, 26, 26, 26, 25, 10, 10, 2, 2, 2, 2, 2, 50, 50, 46, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 248 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/348 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347849840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849840 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 37, 47, 47, 37, 47, 47, 47, 28, 28, 28, 28, 27, 11, 11, 2, 3, 3, 3, 3, 47, 47, 45, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347849840 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 Building ZINC000347849840 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347849840 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 347) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347849840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849840 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 20, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 35, 50, 50, 36, 50, 50, 50, 26, 26, 26, 26, 25, 10, 10, 2, 2, 2, 2, 2, 50, 50, 46, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 248 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 348) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347849840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849840 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 37, 47, 47, 37, 47, 47, 47, 28, 28, 28, 28, 27, 11, 11, 2, 3, 3, 3, 3, 47, 47, 45, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347849840 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849840 Building ZINC000347849842 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347849842 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/349 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849842 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 39, 48, 48, 46, 48, 48, 48, 28, 28, 28, 28, 27, 11, 11, 2, 2, 2, 2, 2, 48, 48, 46, 48] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/350 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849842 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 11, 21, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 36, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 26, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347849842 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 Building ZINC000347849842 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347849842 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 349) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849842 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 39, 48, 48, 46, 48, 48, 48, 28, 28, 28, 28, 27, 11, 11, 2, 2, 2, 2, 2, 48, 48, 46, 48] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 350) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F) `ZINC000347849842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347849842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000347849842 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)Oc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 11, 21, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 21, 36, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 26, 11, 11, 3, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347849842 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849842 Building ZINC000347849891 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347849891 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/351 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347849891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347849891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347849891 none O=C(Nc1ccnn1Cc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 11, 11, 11, 11, 11, 34, 50, 50, 34, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 11, 11, 34, 34, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/352 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1Cc1ccccc1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347849891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347849891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347849891 none O=C(Nc1ccnn1Cc1ccccc1F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 12, 12, 12, 12, 12, 34, 50, 50, 38, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 12, 12, 34, 34, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347849891 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 Building ZINC000347849891 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347849891 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 351) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1Cc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347849891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347849891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347849891 none O=C(Nc1ccnn1Cc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 11, 11, 11, 11, 11, 34, 50, 50, 34, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 11, 11, 34, 34, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 352) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1Cc1ccccc1F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347849891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347849891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347849891 none O=C(Nc1ccnn1Cc1ccccc1F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 12, 12, 12, 12, 12, 34, 50, 50, 38, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 12, 12, 34, 34, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347849891 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347849891 Building ZINC000347850880 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850880 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/353 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850880 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 2, 13, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 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]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/354 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850880 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10] 48 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: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850880 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 Building ZINC000347850880 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850880 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 353) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850880 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 2, 13, 1, 1, 1, 11, 11, 15, 15, 11, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 11, 15, 15, 15, 15, 15, 15, 15, 15] 50 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]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 354) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850880 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10] 48 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: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850880 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850880 Building ZINC000347850882 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850882 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/355 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850882 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [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: 46 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/356 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850882 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850882 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 Building ZINC000347850882 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850882 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 355) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850882 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [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: 46 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 356) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850882 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850882 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850882 Building ZINC000347850884 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850884 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/357 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850884 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10] 49 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/358 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850884 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [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: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850884 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 Building ZINC000347850884 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850884 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 357) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850884 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 10, 10] 49 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 358) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850884 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [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: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850884 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850884 Building ZINC000347850887 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850887 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/359 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850887 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/360 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850887 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [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: 46 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850887 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 Building ZINC000347850887 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347850887 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 359) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347850887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850887 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 360) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000347850887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347850887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347850887 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [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: 46 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347850887 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347850887 Building ZINC000347851607 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851607 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/361 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851607 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/362 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851607 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851607 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 Building ZINC000347851607 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851607 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 361) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851607 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 362) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851607 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851607 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851607 Building ZINC000347851609 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851609 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/363 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851609 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 14, 14, 14, 8, 8, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/364 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851609 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 13, 13, 13, 7, 7, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851609 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 Building ZINC000347851609 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851609 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 363) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851609 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 14, 14, 14, 8, 8, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 364) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl) `ZINC000347851609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851609 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 7, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 13, 13, 13, 7, 7, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851609 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851609 Building ZINC000347851611 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851611 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/365 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851611 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 14, 14, 14, 8, 8, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/366 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851611 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851611 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 Building ZINC000347851611 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851611 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 365) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851611 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 2, 8, 8, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 14, 14, 14, 8, 8, 13, 13, 13, 13, 13, 13, 13, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 366) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851611 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851611 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851611 Building ZINC000347851613 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851613 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/367 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851613 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/368 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851613 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851613 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 Building ZINC000347851613 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347851613 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 367) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347851613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851613 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 368) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl) `ZINC000347851613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347851613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347851613 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](C(F)(F)F)[C@@H]2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 12, 12, 12, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347851613 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347851613 Building ZINC000347852493 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347852493 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/369 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C) `ZINC000347852493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347852493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347852493 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 3, 3, 37, 35, 44, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3, 14, 14, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/370 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C) `ZINC000347852493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347852493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347852493 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 3, 3, 27, 28, 23, 37, 37, 13, 13, 13, 13, 3, 3, 3, 3, 3, 13, 13, 29, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347852493 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 Building ZINC000347852493 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347852493 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 369) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C) `ZINC000347852493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347852493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347852493 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 3, 3, 37, 35, 44, 50, 50, 14, 14, 14, 14, 3, 3, 3, 3, 3, 14, 14, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 370) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C) `ZINC000347852493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347852493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000347852493 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)ccc1C(=O)NC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 3, 3, 27, 28, 23, 37, 37, 13, 13, 13, 13, 3, 3, 3, 3, 3, 13, 13, 29, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347852493 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347852493 Building ZINC000347853913 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347853913 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/371 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1) `ZINC000347853913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347853913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347853913 none Cc1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 27, 27, 27, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 5, 5, 5, 5, 5, 27, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/372 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1) `ZINC000347853913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347853913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347853913 none Cc1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 28, 28, 28, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 5, 5, 5, 5, 5, 28, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347853913 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 Building ZINC000347853913 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347853913 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 371) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1) `ZINC000347853913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347853913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347853913 none Cc1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 27, 27, 27, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 50, 50, 50, 50, 50, 27, 27, 5, 5, 5, 5, 5, 27, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 372) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1) `ZINC000347853913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347853913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347853913 none Cc1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 28, 28, 28, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 5, 5, 5, 5, 5, 28, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347853913 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347853913 Building ZINC000347854702 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854702 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/373 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854702 none CCO[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 30, 21, 21, 21, 21, 10, 21, 4, 6, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 30, 21, 34, 37, 37, 37, 37, 37, 21, 21, 6, 6, 6, 3, 3, 3, 3, 30, 30, 30, 30, 30, 34, 34, 34, 34, 34] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/374 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854702 none CCO[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 21, 21, 21, 21, 12, 21, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 27, 21, 32, 37, 37, 37, 37, 37, 21, 21, 7, 7, 7, 3, 3, 3, 3, 27, 27, 27, 27, 27, 32, 32, 32, 32, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854702 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 Building ZINC000347854702 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854702 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 373) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854702 none CCO[C@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 30, 21, 21, 21, 21, 10, 21, 4, 6, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 30, 21, 34, 37, 37, 37, 37, 37, 21, 21, 6, 6, 6, 3, 3, 3, 3, 30, 30, 30, 30, 30, 34, 34, 34, 34, 34] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 374) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854702 none CCO[C@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 21, 21, 21, 21, 12, 21, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 27, 21, 32, 37, 37, 37, 37, 37, 21, 21, 7, 7, 7, 3, 3, 3, 3, 27, 27, 27, 27, 27, 32, 32, 32, 32, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854702 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854702 Building ZINC000347854707 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854707 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/375 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854707 none CCO[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 21, 21, 21, 21, 10, 21, 4, 7, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 21, 21, 31, 21, 26, 37, 37, 37, 37, 37, 21, 21, 7, 7, 7, 5, 5, 5, 5, 31, 31, 31, 31, 31, 26, 26, 26, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/376 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854707 none CCO[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 18, 27, 18, 22, 44, 44, 44, 44, 44, 18, 18, 6, 6, 6, 4, 4, 4, 4, 27, 27, 27, 27, 27, 22, 22, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854707 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 Building ZINC000347854707 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854707 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 375) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854707 none CCO[C@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 21, 21, 21, 21, 10, 21, 4, 7, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 21, 21, 31, 21, 26, 37, 37, 37, 37, 37, 21, 21, 7, 7, 7, 5, 5, 5, 5, 31, 31, 31, 31, 31, 26, 26, 26, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 376) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854707 none CCO[C@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 18, 18, 18, 18, 8, 18, 4, 6, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 18, 18, 27, 18, 22, 44, 44, 44, 44, 44, 18, 18, 6, 6, 6, 4, 4, 4, 4, 27, 27, 27, 27, 27, 22, 22, 22, 22, 22] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854707 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854707 Building ZINC000347854711 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854711 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/377 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854711 none CCO[C@@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 19, 19, 19, 8, 19, 4, 6, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 23, 19, 28, 42, 42, 42, 42, 42, 19, 19, 6, 6, 6, 3, 3, 3, 3, 23, 23, 23, 23, 23, 28, 28, 28, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/378 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854711 none CCO[C@@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 21, 21, 21, 21, 10, 21, 4, 7, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 26, 21, 32, 38, 38, 38, 38, 38, 21, 21, 7, 7, 7, 4, 4, 4, 4, 26, 26, 26, 26, 26, 32, 32, 32, 32, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854711 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 Building ZINC000347854711 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854711 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 377) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854711 none CCO[C@@H]1C[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 19, 19, 19, 8, 19, 4, 6, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 19, 19, 23, 19, 28, 42, 42, 42, 42, 42, 19, 19, 6, 6, 6, 3, 3, 3, 3, 23, 23, 23, 23, 23, 28, 28, 28, 28, 28] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 378) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854711 none CCO[C@@H]1C[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 21, 21, 21, 21, 10, 21, 4, 7, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 21, 21, 26, 21, 32, 38, 38, 38, 38, 38, 21, 21, 7, 7, 7, 4, 4, 4, 4, 26, 26, 26, 26, 26, 32, 32, 32, 32, 32] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854711 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854711 Building ZINC000347854717 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854717 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/379 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854717 none CCO[C@@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 21, 21, 21, 21, 12, 21, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 32, 21, 27, 36, 36, 36, 36, 36, 21, 21, 7, 7, 7, 3, 3, 3, 3, 32, 32, 32, 32, 32, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/380 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854717 none CCO[C@@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 22, 22, 22, 22, 11, 22, 5, 7, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 35, 22, 31, 36, 36, 36, 36, 36, 22, 22, 7, 7, 7, 3, 3, 3, 3, 35, 35, 35, 35, 35, 31, 31, 31, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854717 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 Building ZINC000347854717 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347854717 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 379) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347854717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854717 none CCO[C@@H]1C[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 21, 21, 21, 21, 12, 21, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 32, 21, 27, 36, 36, 36, 36, 36, 21, 21, 7, 7, 7, 3, 3, 3, 3, 32, 32, 32, 32, 32, 27, 27, 27, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 380) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC) `ZINC000347854717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347854717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000347854717 none CCO[C@@H]1C[C@H](N(C)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1(CC)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 22, 22, 22, 22, 11, 22, 5, 7, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 35, 22, 31, 36, 36, 36, 36, 36, 22, 22, 7, 7, 7, 3, 3, 3, 3, 35, 35, 35, 35, 35, 31, 31, 31, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347854717 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347854717 Building ZINC000347856721 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347856721 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/381 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347856721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347856721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347856721 none CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 22, 22, 22, 22, 22, 22, 22, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 35, 35, 22, 22, 22, 13, 13, 3, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 177 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/382 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347856721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347856721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347856721 none CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 22, 22, 22, 14, 13, 22, 22, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 36, 36, 22, 22, 22, 13, 13, 3, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 202 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347856721 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 Building ZINC000347856721 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347856721 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 381) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347856721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347856721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347856721 none CSCc1cc(F)ccc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 22, 22, 22, 22, 22, 22, 22, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 35, 35, 22, 22, 22, 13, 13, 3, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 177 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 382) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347856721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347856721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347856721 none CSCc1cc(F)ccc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 22, 22, 22, 14, 13, 22, 22, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 36, 36, 22, 22, 22, 13, 13, 3, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 202 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347856721 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347856721 Building ZINC000347857257 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347857257 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/383 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)cn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347857257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347857257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347857257 none O=C(Nc1ccc(N2CCCCC2)cn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 18, 50, 50, 50, 50, 46, 10, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/384 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)cn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347857257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347857257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347857257 none O=C(Nc1ccc(N2CCCCC2)cn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 18, 50, 50, 50, 50, 46, 10, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347857257 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 Building ZINC000347857257 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347857257 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 383) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)cn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347857257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347857257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347857257 none O=C(Nc1ccc(N2CCCCC2)cn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 18, 50, 50, 50, 50, 46, 10, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 384) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)cn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347857257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347857257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347857257 none O=C(Nc1ccc(N2CCCCC2)cn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 18, 50, 50, 50, 50, 46, 10, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347857257 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857257 Building ZINC000347857935 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347857935 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/385 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347857935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347857935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347857935 none Cc1ccnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 12, 50, 50, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 50, 50, 50, 50, 12, 50, 12, 12, 12, 2, 3, 3, 3, 3, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/386 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347857935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347857935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347857935 none Cc1ccnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 20, 50, 50, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 50, 50, 50, 50, 42, 50, 12, 12, 12, 2, 3, 3, 3, 3, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347857935 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 Building ZINC000347857935 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347857935 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 385) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347857935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347857935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347857935 none Cc1ccnc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 12, 50, 50, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 50, 50, 50, 50, 12, 50, 12, 12, 12, 2, 3, 3, 3, 3, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 386) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1) `ZINC000347857935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347857935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347857935 none Cc1ccnc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 20, 50, 50, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 50, 50, 50, 50, 42, 50, 12, 12, 12, 2, 3, 3, 3, 3, 12] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347857935 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347857935 Building ZINC000347859272 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859272 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/387 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347859272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347859272 none CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 23, 23, 23, 16, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 2, 5, 5, 46, 46, 46, 46, 23, 23, 23, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/388 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347859272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347859272 none CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 23, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 46, 23, 23, 23, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859272 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 Building ZINC000347859272 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859272 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 387) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347859272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347859272 none CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 23, 23, 23, 16, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 2, 5, 5, 46, 46, 46, 46, 23, 23, 23, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 388) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347859272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347859272 none CC(=O)Nc1cc(Cl)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 23, 23, 23, 23, 23, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 46, 46, 46, 46, 23, 23, 23, 5, 5, 5, 5, 5] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859272 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859272 Building ZINC000347859672 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859672 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/389 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859672 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 8, 8] 44 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/390 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859672 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 9] 48 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]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859672 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 Building ZINC000347859672 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859672 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 389) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859672 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 8, 8] 44 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 390) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859672 none C[C@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 9] 48 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]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859672 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859672 Building ZINC000347859673 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859673 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/391 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859673 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11] 47 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/392 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859673 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859673 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 Building ZINC000347859673 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859673 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 391) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859673 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11] 47 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 392) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859673 none C[C@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859673 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859673 Building ZINC000347859674 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859674 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/393 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859674 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10] 48 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]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/394 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859674 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 8, 8] 44 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859674 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 Building ZINC000347859674 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859674 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 393) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859674 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 10, 10] 48 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]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 394) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859674 none C[C@@H]1[C@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 8, 8] 44 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859674 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859674 Building ZINC000347859675 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859675 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/395 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859675 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/396 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859675 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11] 48 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859675 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 Building ZINC000347859675 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347859675 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 395) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347859675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859675 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 396) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000347859675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347859675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000347859675 none C[C@@H]1[C@@H](C(F)(F)F)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 5, 15, 15, 15, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 11, 11] 48 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347859675 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347859675 Building ZINC000347861577 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347861577 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/397 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1) `ZINC000347861577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347861577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347861577 none Cc1ccnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 21, 45, 35, 6, 6, 31, 31, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 36, 45, 45, 45, 26, 45, 31, 31, 6, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/398 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1) `ZINC000347861577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347861577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347861577 none Cc1ccnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 49, 49, 29, 21, 30, 30, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 49, 49, 49, 49, 30, 49, 30, 30, 6, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347861577 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 Building ZINC000347861577 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347861577 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 397) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1) `ZINC000347861577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347861577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347861577 none Cc1ccnc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 21, 45, 35, 6, 6, 31, 31, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 36, 45, 45, 45, 26, 45, 31, 31, 6, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 398) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1) `ZINC000347861577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347861577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000347861577 none Cc1ccnc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 49, 49, 29, 21, 30, 30, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 49, 49, 49, 49, 30, 49, 30, 30, 6, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347861577 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347861577 Building ZINC000347862805 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347862805 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/399 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347862805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347862805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347862805 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 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: [49, 49, 30, 49, 30, 30, 30, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 49, 49, 49, 30, 30, 6, 5, 5, 5, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/400 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347862805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347862805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347862805 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 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: [49, 49, 30, 49, 30, 30, 30, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 4, 5, 5, 30, 30, 30, 49, 49, 49, 30, 30, 6, 5, 5, 5, 5, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347862805 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 Building ZINC000347862805 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347862805 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 399) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347862805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347862805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347862805 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 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: [49, 49, 30, 49, 30, 30, 30, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 49, 49, 49, 30, 30, 6, 5, 5, 5, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 400) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl) `ZINC000347862805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347862805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000347862805 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 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: [49, 49, 30, 49, 30, 30, 30, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 4, 5, 5, 30, 30, 30, 49, 49, 49, 30, 30, 6, 5, 5, 5, 5, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347862805 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347862805 Building ZINC000347868804 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347868804 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/401 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347868804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347868804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347868804 none COc1ccc(OC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 13, 13, 36, 44, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 19, 19, 19, 13, 13, 44, 44, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/402 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347868804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347868804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347868804 none COc1ccc(OC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 13, 13, 36, 44, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 19, 19, 19, 13, 13, 44, 44, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347868804 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 Building ZINC000347868804 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347868804 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 401) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(OC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347868804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347868804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347868804 none COc1ccc(OC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 13, 13, 36, 44, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 19, 19, 19, 13, 13, 44, 44, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 402) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(OC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347868804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347868804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347868804 none COc1ccc(OC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 13, 13, 36, 44, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 19, 19, 19, 13, 13, 44, 44, 44, 44, 44, 44, 44, 4, 3, 3, 3, 3, 13] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347868804 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347868804 Building ZINC000347914998 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347914998 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/403 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CCN2CCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347914998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347914998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347914998 none O=C(Nc1cccc(CCN2CCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 10, 14, 14, 29, 29, 50, 50, 50, 50, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 14, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/404 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CCN2CCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347914998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347914998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347914998 none O=C(Nc1cccc(CCN2CCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 3, 14, 14, 28, 28, 50, 50, 50, 50, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 6, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347914998 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 Building ZINC000347914998 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347914998 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 403) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(CCN2CCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347914998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347914998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347914998 none O=C(Nc1cccc(CCN2CCCC2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 10, 14, 14, 29, 29, 50, 50, 50, 50, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 14, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 404) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(CCN2CCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347914998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347914998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347914998 none O=C(Nc1cccc(CCN2CCCC2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 5, 10, 5, 5, 5, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 14, 3, 14, 14, 28, 28, 50, 50, 50, 50, 14, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 6, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 14, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347914998 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347914998 Building ZINC000347919960 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347919960 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/405 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2cccs2)ns1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347919960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347919960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347919960 none O=C(Nc1nc(c2cccs2)ns1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 14, 8, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 50, 50, 50, 50, 11, 11, 1, 1, 1, 5, 5, 2, 3, 5, 5, 6, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/406 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2cccs2)ns1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347919960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347919960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347919960 none O=C(Nc1nc(c2cccs2)ns1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 14, 8, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 50, 50, 50, 50, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347919960 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 Building ZINC000347919960 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347919960 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 405) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(c2cccs2)ns1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347919960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347919960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347919960 none O=C(Nc1nc(c2cccs2)ns1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 14, 8, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 50, 50, 50, 50, 11, 11, 1, 1, 1, 5, 5, 2, 3, 5, 5, 6, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 406) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(c2cccs2)ns1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347919960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347919960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347919960 none O=C(Nc1nc(c2cccs2)ns1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 14, 8, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 50, 50, 50, 50, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347919960 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347919960 Building ZINC000347900333 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347900333 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/407 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347900333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347900333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347900333 none COc1ccc2c(c1)CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 2, 22, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/408 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347900333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347900333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347900333 none COc1ccc2c(c1)CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 32, 32, 32, 32, 32, 16, 2, 23, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347900333 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 Building ZINC000347900333 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347900333 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 407) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc2c(c1)CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347900333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347900333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347900333 none COc1ccc2c(c1)CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 2, 22, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 408) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc2c(c1)CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347900333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347900333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000347900333 none COc1ccc2c(c1)CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 32, 32, 32, 32, 32, 16, 2, 23, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347900333 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347900333 Building ZINC000347904834 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347904834 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/409 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc21) `ZINC000347904834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347904834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347904834 none COCCn1ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 30, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 48, 48, 30, 30, 15, 15, 15, 15, 3, 3, 3, 3, 3, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/410 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc21) `ZINC000347904834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347904834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347904834 none COCCn1ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 31, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 48, 48, 31, 31, 15, 15, 15, 15, 3, 3, 3, 3, 3, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347904834 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 Building ZINC000347904834 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347904834 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 409) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCn1ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc21) `ZINC000347904834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347904834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347904834 none COCCn1ccc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 30, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 48, 48, 30, 30, 15, 15, 15, 15, 3, 3, 3, 3, 3, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 410) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCn1ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc21) `ZINC000347904834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347904834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347904834 none COCCn1ccc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 31, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 50, 50, 50, 48, 48, 31, 31, 15, 15, 15, 15, 3, 3, 3, 3, 3, 15] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347904834 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347904834 Building ZINC000347910307 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347910307 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/411 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OCC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347910307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347910307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347910307 none O=C(Nc1ccc(F)cc1OCC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 30, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 10, 10, 10, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/412 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1OCC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347910307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347910307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347910307 none O=C(Nc1ccc(F)cc1OCC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 6, 10, 10, 10, 10, 31, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 10, 10, 10, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347910307 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 Building ZINC000347910307 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347910307 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 411) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(F)cc1OCC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347910307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347910307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347910307 none O=C(Nc1ccc(F)cc1OCC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 30, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 10, 10, 10, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 412) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(F)cc1OCC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347910307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347910307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347910307 none O=C(Nc1ccc(F)cc1OCC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 12, 5, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 6, 10, 10, 10, 10, 31, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 10, 10, 10, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347910307 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347910307 Building ZINC000347911800 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347911800 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/413 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347911800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347911800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347911800 none O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 9, 34, 34, 50, 50, 50, 50, 9, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 34, 34, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/414 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347911800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347911800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347911800 none O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 9, 35, 35, 50, 50, 50, 50, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 35, 35, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347911800 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 Building ZINC000347911800 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347911800 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 413) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347911800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347911800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347911800 none O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 9, 34, 34, 50, 50, 50, 50, 9, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 34, 34, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 414) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347911800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347911800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347911800 none O=C(Nc1nnc(/C=C/c2ccco2)s1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 9, 9, 9, 9, 35, 35, 50, 50, 50, 50, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 35, 35, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347911800 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347911800 Building ZINC000347946729 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347946729 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/415 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2cc(F)ccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347946729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347946729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347946729 none CCn1c2cc(F)ccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 17, 17, 17, 7, 6, 6, 6, 6] 33 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: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/416 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2cc(F)ccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347946729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347946729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347946729 none CCn1c2cc(F)ccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 17, 17, 17, 7, 6, 6, 6, 6] 33 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: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347946729 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 Building ZINC000347946729 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347946729 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 415) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1c2cc(F)ccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347946729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347946729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347946729 none CCn1c2cc(F)ccc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 17, 17, 17, 7, 6, 6, 6, 6] 33 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: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 416) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1c2cc(F)ccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347946729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347946729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347946729 none CCn1c2cc(F)ccc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 15, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 31, 31, 31, 31, 31, 17, 17, 17, 7, 6, 6, 6, 6] 33 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: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347946729 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347946729 Building ZINC000347926801 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347926801 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/417 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1) `ZINC000347926801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347926801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347926801 none Cn1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 33, 33, 46, 46, 33, 33, 33, 33, 33, 6, 5, 5, 5, 5, 33, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/418 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1) `ZINC000347926801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347926801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347926801 none Cn1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 32, 45, 45, 32, 32, 32, 32, 32, 6, 5, 5, 5, 5, 32, 45, 45, 45, 45, 45] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347926801 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 Building ZINC000347926801 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347926801 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 417) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1) `ZINC000347926801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347926801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347926801 none Cn1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 33, 33, 33, 33, 33, 46, 46, 33, 33, 33, 33, 33, 6, 5, 5, 5, 5, 33, 46, 46, 46, 46, 46] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 418) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1) `ZINC000347926801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347926801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000347926801 none Cn1c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2nc1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 32, 45, 45, 32, 32, 32, 32, 32, 6, 5, 5, 5, 5, 32, 45, 45, 45, 45, 45] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/318708/xbg-8058115.33/working/building/ZINC000347926801 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347926801 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347926801 Building ZINC000347927832 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347927832 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/419 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccc(F)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347927832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347927832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347927832 none CCn1c2ccc(F)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 17, 17, 17, 8, 6, 6, 6, 6] 34 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: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/420 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccc(F)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347927832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347927832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347927832 none CCn1c2ccc(F)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 17, 17, 17, 8, 6, 6, 6, 6] 34 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: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347927832 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 Building ZINC000347927832 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347927832 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 419) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1c2ccc(F)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347927832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347927832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347927832 none CCn1c2ccc(F)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 17, 17, 17, 8, 6, 6, 6, 6] 34 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: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 420) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1c2ccc(F)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347927832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347927832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000347927832 none CCn1c2ccc(F)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 17, 17, 17, 8, 6, 6, 6, 6] 34 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: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347927832 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347927832 Building ZINC000347929950 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347929950 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/421 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccnc2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347929950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347929950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347929950 none O=C(Nc1ccc(Oc2cccnc2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 27, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 50, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/422 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2cccnc2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347929950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347929950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347929950 none O=C(Nc1ccc(Oc2cccnc2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 27, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 50, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347929950 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 Building ZINC000347929950 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347929950 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 421) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(Oc2cccnc2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347929950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347929950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347929950 none O=C(Nc1ccc(Oc2cccnc2)nc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 27, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 50, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 422) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(Oc2cccnc2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347929950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347929950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000347929950 none O=C(Nc1ccc(Oc2cccnc2)nc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 8, 8, 8, 27, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 50, 50, 50, 50, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347929950 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347929950 Building ZINC000347932211 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347932211 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/423 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccc(C)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347932211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347932211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347932211 none CCn1c2ccc(C)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 17, 17, 17, 17, 17, 17, 8, 6, 6, 6, 6] 34 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/424 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccc(C)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347932211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347932211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347932211 none CCn1c2ccc(C)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 8, 6, 6, 6, 6] 35 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347932211 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 Building ZINC000347932211 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347932211 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 423) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1c2ccc(C)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347932211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347932211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347932211 none CCn1c2ccc(C)cc2nc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 32, 17, 17, 17, 17, 17, 17, 8, 6, 6, 6, 6] 34 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 424) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1c2ccc(C)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347932211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347932211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347932211 none CCn1c2ccc(C)cc2nc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 33, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 8, 6, 6, 6, 6] 35 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347932211 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347932211 Building ZINC000347934694 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347934694 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/425 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347934694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347934694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347934694 none CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 18, 47, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/426 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347934694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347934694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347934694 none CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 18, 47, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347934694 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 Building ZINC000347934694 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347934694 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 425) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347934694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347934694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347934694 none CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 18, 47, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 426) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347934694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347934694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347934694 none CCOC(=O)c1ccc(F)c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 18, 47, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347934694 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347934694 Building ZINC000347966900 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347966900 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/427 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347966900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347966900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347966900 none O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 1, 1, 1, 5, 5, 2, 2, 5, 5, 6, 13, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/428 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347966900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347966900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347966900 none O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 13, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347966900 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 Building ZINC000347966900 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347966900 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 427) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347966900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347966900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347966900 none O=C(Nc1csc(c2ccccn2)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 1, 1, 1, 5, 5, 2, 2, 5, 5, 6, 13, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 428) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347966900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347966900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000347966900 none O=C(Nc1csc(c2ccccn2)n1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 13, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347966900 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347966900 Building ZINC000347976892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347976892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/429 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/430 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/431 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/431' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/432 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/432' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347976892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 Building ZINC000347976892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347976892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 429) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 430) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 431) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 432) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347976892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 Building ZINC000347976892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347976892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 429) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 430) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 431) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 432) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347976892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 Building ZINC000347976892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000347976892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 429) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 430) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 431) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 432) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347976892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000347976892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000347976892 none O=C(NC[C@H]1CC[N@@](c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 18, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 10, 10, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347976892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347976892 Building ZINC000347978276 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347978276 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/433 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347978276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347978276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347978276 none CCCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 25, 25, 25, 25, 25, 18, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 50, 50, 50, 50, 50, 48, 48, 25, 25, 25, 18, 18, 10, 10, 2, 3, 3, 3, 3, 25] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/434 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347978276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347978276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347978276 none CCCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 25, 25, 25, 25, 25, 18, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 50, 50, 50, 50, 50, 48, 48, 25, 25, 25, 18, 18, 10, 10, 2, 3, 3, 3, 3, 25] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347978276 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 Building ZINC000347978276 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347978276 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 433) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347978276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347978276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347978276 none CCCOc1cccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 25, 25, 25, 25, 25, 18, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 50, 50, 50, 50, 50, 48, 48, 25, 25, 25, 18, 18, 10, 10, 2, 3, 3, 3, 3, 25] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 434) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347978276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347978276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000347978276 none CCCOc1cccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 45, 25, 25, 25, 25, 25, 18, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 50, 50, 50, 50, 50, 48, 48, 25, 25, 25, 18, 18, 10, 10, 2, 3, 3, 3, 3, 25] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347978276 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978276 Building ZINC000347978288 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347978288 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/435 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000347978288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347978288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347978288 none CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 44, 44, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/436 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000347978288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347978288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347978288 none CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 44, 44, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347978288 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 Building ZINC000347978288 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347978288 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 435) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000347978288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347978288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347978288 none CCCOc1ccc2c(c1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 44, 44, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 436) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2) `ZINC000347978288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347978288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000347978288 none CCCOc1ccc2c(c1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 50, 50, 50, 50, 50, 44, 44, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347978288 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978288 Building ZINC000347978323 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347978323 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/437 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1) `ZINC000347978323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347978323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347978323 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 44, 44, 34, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 50, 50, 50, 44, 44, 34, 34, 17, 17, 3, 3, 3, 3, 3, 44] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/438 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1) `ZINC000347978323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347978323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347978323 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 43, 34, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 50, 50, 50, 43, 43, 34, 34, 17, 17, 3, 3, 3, 3, 3, 43] 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]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347978323 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 Building ZINC000347978323 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347978323 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 437) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1) `ZINC000347978323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347978323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347978323 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 44, 44, 34, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 50, 50, 50, 44, 44, 34, 34, 17, 17, 3, 3, 3, 3, 3, 44] 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 438) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1) `ZINC000347978323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347978323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347978323 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 43, 34, 17, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 50, 50, 50, 43, 43, 34, 34, 17, 17, 3, 3, 3, 3, 3, 43] 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]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347978323 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347978323 Building ZINC000347981395 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347981395 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/439 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347981395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347981395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347981395 none Cn1nc(C2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 19, 50, 50, 50, 50, 50, 13, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 8, 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, 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/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/440 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(C2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347981395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347981395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347981395 none Cn1nc(C2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 16, 50, 50, 50, 50, 50, 10, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 6, 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347981395 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 Building ZINC000347981395 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347981395 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 439) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1nc(C2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347981395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347981395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347981395 none Cn1nc(C2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 19, 50, 50, 50, 50, 50, 13, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 8, 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, 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/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 440) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1nc(C2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347981395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347981395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000347981395 none Cn1nc(C2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 16, 50, 50, 50, 50, 50, 10, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 6, 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347981395 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347981395 Building ZINC000347983191 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347983191 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/441 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F) `ZINC000347983191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347983191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347983191 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 16, 16, 16, 16, 42, 42, 18, 42, 42, 42, 16, 16, 16, 5, 5, 5, 5, 5, 16, 42, 42, 42, 42] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/442 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F) `ZINC000347983191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347983191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347983191 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 15, 15, 15, 42, 42, 22, 42, 42, 42, 15, 15, 15, 5, 5, 5, 5, 5, 15, 42, 42, 42, 42] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347983191 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 Building ZINC000347983191 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347983191 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 441) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F) `ZINC000347983191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347983191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347983191 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 5, 5, 1, 5, 1, 1, 1, 5, 5, 2, 5, 5, 5, 16, 16, 16, 16, 42, 42, 18, 42, 42, 42, 16, 16, 16, 5, 5, 5, 5, 5, 16, 42, 42, 42, 42] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 442) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F) `ZINC000347983191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347983191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000347983191 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cnn1c1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 15, 15, 15, 42, 42, 22, 42, 42, 42, 15, 15, 15, 5, 5, 5, 5, 5, 15, 42, 42, 42, 42] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347983191 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347983191 Building ZINC000347988477 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347988477 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/443 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347988477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347988477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347988477 none Cc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 47, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 39, 39, 39, 39, 39, 39, 50, 15, 15, 3, 2, 2, 2, 2, 39] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/444 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347988477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347988477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347988477 none Cc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 47, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 39, 39, 39, 39, 39, 39, 50, 15, 15, 3, 2, 2, 2, 2, 39] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347988477 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 Building ZINC000347988477 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347988477 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 443) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347988477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347988477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347988477 none Cc1ccc(OC(F)F)c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 47, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 39, 39, 39, 39, 39, 39, 50, 15, 15, 3, 2, 2, 2, 2, 39] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 444) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000347988477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347988477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347988477 none Cc1ccc(OC(F)F)c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 47, 50, 50, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 39, 39, 39, 39, 39, 39, 50, 15, 15, 3, 2, 2, 2, 2, 39] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347988477 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347988477 Building ZINC000347989079 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347989079 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/445 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1) `ZINC000347989079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347989079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989079 none CCc1cc(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 24, 24, 24, 24, 24, 24, 24, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 2, 5, 5, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 24, 24, 4, 5, 5, 5, 5, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/446 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1) `ZINC000347989079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347989079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989079 none CCc1cc(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 24, 24, 24, 24, 24, 24, 24, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 24, 24, 4, 5, 5, 5, 5, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347989079 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 Building ZINC000347989079 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347989079 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 445) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1) `ZINC000347989079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347989079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989079 none CCc1cc(=O)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 24, 24, 24, 24, 24, 24, 24, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 2, 5, 5, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 24, 24, 4, 5, 5, 5, 5, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 446) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1) `ZINC000347989079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347989079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989079 none CCc1cc(=O)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)ccc2[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 24, 24, 24, 24, 24, 24, 24, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 24, 24, 4, 5, 5, 5, 5, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347989079 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989079 Building ZINC000347989095 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347989095 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/447 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347989095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347989095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989095 none O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 38, 38, 38, 50, 50, 50, 50, 38, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/448 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347989095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347989095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989095 none O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 38, 38, 38, 50, 50, 50, 50, 38, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347989095 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 Building ZINC000347989095 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347989095 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 447) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347989095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347989095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989095 none O=C(NCc1cccc(c2ccccn2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 38, 38, 38, 50, 50, 50, 50, 38, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 448) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347989095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347989095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000347989095 none O=C(NCc1cccc(c2ccccn2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 11, 11, 38, 38, 38, 50, 50, 50, 50, 38, 2, 2, 2, 2] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347989095 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347989095 Building ZINC000347993131 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347993131 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/449 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1) `ZINC000347993131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347993131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347993131 none Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 9, 6, 6, 6, 6, 26] 33 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/450 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1) `ZINC000347993131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347993131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347993131 none Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 9, 6, 6, 6, 6, 26] 33 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347993131 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 Building ZINC000347993131 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347993131 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 449) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1) `ZINC000347993131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347993131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347993131 none Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 9, 6, 6, 6, 6, 26] 33 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 450) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1) `ZINC000347993131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347993131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000347993131 none Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 9, 6, 6, 6, 6, 26] 33 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347993131 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347993131 Building ZINC000347998823 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347998823 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/451 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347998823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998823 none C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 3, 3, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 19 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/452 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347998823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998823 none C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 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: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4] 22 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347998823 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 Building ZINC000347998823 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347998823 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 451) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347998823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998823 none C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 3, 3, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 19 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 452) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347998823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998823 none C[C@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 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: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 4, 4, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4] 22 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347998823 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998823 Building ZINC000347998828 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347998828 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/453 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347998828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998828 none C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 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: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 4, 4, 1, 3, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4] 22 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/454 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347998828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998828 none C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 19 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347998828 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 Building ZINC000347998828 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347998828 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 453) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347998828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998828 none C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 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: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 4, 4, 1, 3, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4] 22 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 454) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000347998828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347998828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347998828 none C[C@@H]1c2cc(F)cc(F)c2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', '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: [5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3] 19 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000347998828 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000347998828 Building ZINC000348002959 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348002959 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/455 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348002959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348002959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348002959 none COc1cccc2c1CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 18, 2, 26, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/456 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc2c1CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348002959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348002959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348002959 none COc1cccc2c1CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 2, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348002959 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 Building ZINC000348002959 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348002959 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 455) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc2c1CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348002959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348002959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348002959 none COc1cccc2c1CCCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 18, 2, 26, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 456) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc2c1CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348002959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348002959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348002959 none COc1cccc2c1CCCCN2C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 2, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348002959 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348002959 Building ZINC000348007173 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348007173 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/457 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(C)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000348007173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348007173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348007173 none Cc1cnn(c2ccc(C)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 13, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 50] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/458 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(c2ccc(C)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000348007173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348007173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348007173 none Cc1cnn(c2ccc(C)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 13, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 50] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348007173 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 Building ZINC000348007173 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348007173 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 457) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000348007173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348007173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348007173 none Cc1cnn(c2ccc(C)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 13, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 5, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 50] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 458) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000348007173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348007173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348007173 none Cc1cnn(c2ccc(C)cc2NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 13, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21, 21, 6, 5, 5, 5, 5, 50] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348007173 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348007173 Building ZINC000348013348 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348013348 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/459 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)ccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348013348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348013348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000348013348 none O=C(Nc1cc(F)ccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 12, 16, 16, 16, 38, 50, 50, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 16, 13, 16, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/460 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)ccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348013348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348013348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000348013348 none O=C(Nc1cc(F)ccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 10, 15, 15, 15, 37, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 10, 15, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348013348 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 Building ZINC000348013348 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348013348 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 459) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cc(F)ccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348013348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348013348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000348013348 none O=C(Nc1cc(F)ccc1OC(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 12, 16, 16, 16, 38, 50, 50, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 16, 13, 16, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 460) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cc(F)ccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348013348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348013348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000348013348 none O=C(Nc1cc(F)ccc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 10, 15, 15, 15, 37, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 15, 10, 15, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348013348 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013348 Building ZINC000348013872 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348013872 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/461 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348013872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013872 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 26, 26, 12, 26, 26, 26, 48, 48, 48, 48, 12, 12, 12, 6, 4, 4, 4, 4, 26, 26, 26, 26, 48, 48, 48] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/462 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348013872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013872 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 25, 25, 12, 25, 25, 25, 50, 50, 50, 50, 12, 12, 12, 6, 3, 3, 3, 3, 25, 25, 25, 25, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348013872 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 Building ZINC000348013872 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348013872 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 461) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348013872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013872 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 12, 26, 26, 12, 26, 26, 26, 48, 48, 48, 48, 12, 12, 12, 6, 4, 4, 4, 4, 26, 26, 26, 26, 48, 48, 48] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 462) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348013872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013872 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 25, 25, 12, 25, 25, 25, 50, 50, 50, 50, 12, 12, 12, 6, 3, 3, 3, 3, 25, 25, 25, 25, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348013872 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013872 Building ZINC000348013877 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348013877 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/463 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348013877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013877 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 11, 24, 24, 11, 24, 24, 24, 50, 50, 50, 50, 11, 11, 11, 6, 3, 3, 3, 3, 24, 24, 24, 24, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/464 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348013877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013877 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 26, 26, 12, 26, 26, 26, 50, 50, 50, 50, 12, 12, 12, 6, 3, 3, 3, 3, 26, 26, 26, 26, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348013877 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 Building ZINC000348013877 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348013877 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 463) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348013877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013877 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 11, 24, 24, 11, 24, 24, 24, 50, 50, 50, 50, 11, 11, 11, 6, 3, 3, 3, 3, 24, 24, 24, 24, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 464) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1) `ZINC000348013877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348013877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348013877 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 26, 26, 12, 26, 26, 26, 50, 50, 50, 50, 12, 12, 12, 6, 3, 3, 3, 3, 26, 26, 26, 26, 50, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348013877 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348013877 Building ZINC000348015387 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348015387 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/465 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCCC2) `ZINC000348015387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348015387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000348015387 none COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 18, 2, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/466 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCCC2) `ZINC000348015387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348015387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000348015387 none COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 36, 36, 36, 19, 2, 26, 1, 1, 1, 4, 4, 1, 2, 4, 4, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348015387 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 Building ZINC000348015387 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348015387 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 465) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCCC2) `ZINC000348015387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348015387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000348015387 none COc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 35, 18, 2, 25, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 49, 49, 49, 35, 35, 35, 5, 5, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 466) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCCC2) `ZINC000348015387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348015387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000348015387 none COc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 36, 36, 36, 19, 2, 26, 1, 1, 1, 4, 4, 1, 2, 4, 4, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348015387 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348015387 Building ZINC000348017042 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348017042 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/467 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348017042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348017042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348017042 none CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 15, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 15, 15, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/468 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348017042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348017042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348017042 none CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 15, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 15, 15, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348017042 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 Building ZINC000348017042 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348017042 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 467) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348017042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348017042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348017042 none CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 15, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 15, 15, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 468) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348017042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348017042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000348017042 none CN(Cc1ncc(c2ccccc2)[nH]1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 15, 28, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 15, 15, 28, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348017042 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348017042 Building ZINC000348031167 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348031167 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/469 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348031167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348031167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348031167 none O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 30, 30, 30, 30, 30, 30, 48, 48, 30, 30, 30, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 30, 30, 48, 30, 5, 5, 5, 5] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/470 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348031167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348031167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348031167 none O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 30, 30, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 30, 30, 50, 30, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348031167 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 Building ZINC000348031167 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348031167 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 469) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348031167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348031167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348031167 none O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 30, 30, 30, 30, 30, 30, 48, 48, 30, 30, 30, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 30, 30, 48, 30, 5, 5, 5, 5] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 470) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348031167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348031167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348031167 none O=C(Nc1ccc2nc(C(F)F)[nH]c2c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 5, 15, 15, 8, 6, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 30, 30, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 30, 30, 50, 30, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348031167 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348031167 Building ZINC000348035913 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348035913 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/471 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348035913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348035913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348035913 none Cc1cc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 7, 6, 6, 6, 6] 28 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/472 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348035913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348035913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348035913 none Cc1cc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 7, 6, 6, 6, 6] 28 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348035913 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 Building ZINC000348035913 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348035913 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 471) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348035913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348035913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348035913 none Cc1cc(Br)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 7, 6, 6, 6, 6] 28 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 472) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348035913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348035913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348035913 none Cc1cc(Br)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 7, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 26, 26, 26, 26, 26, 7, 6, 6, 6, 6] 28 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348035913 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348035913 Building ZINC000348072685 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348072685 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/473 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCCc3ccccc32)cn1) `ZINC000348072685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348072685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348072685 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 7, 7, 1, 1, 1, 2, 10, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/474 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCCc3ccccc32)cn1) `ZINC000348072685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348072685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348072685 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 12, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348072685 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 Building ZINC000348072685 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348072685 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 473) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2CCCCc3ccccc32)cn1) `ZINC000348072685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348072685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348072685 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 10, 7, 7, 1, 1, 1, 2, 10, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 474) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)N2CCCCc3ccccc32)cn1) `ZINC000348072685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348072685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348072685 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 12, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348072685 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348072685 Building ZINC000348044303 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348044303 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/475 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F) `ZINC000348044303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348044303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348044303 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 7, 17, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 7, 6, 6, 6, 6] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/476 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F) `ZINC000348044303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348044303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348044303 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 8, 24, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 24, 24, 35, 35, 35, 35, 35, 8, 6, 6, 6, 6] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348044303 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 Building ZINC000348044303 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348044303 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 475) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F) `ZINC000348044303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348044303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348044303 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 7, 17, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 7, 6, 6, 6, 6] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 476) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F) `ZINC000348044303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348044303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000348044303 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 8, 24, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 24, 24, 24, 24, 35, 35, 35, 35, 35, 8, 6, 6, 6, 6] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348044303 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348044303 Building ZINC000348055441 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348055441 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/477 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000348055441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348055441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000348055441 none CC(C)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 4, 4, 28, 28, 24, 28, 28, 28, 28, 22, 22, 20, 20, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/478 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000348055441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348055441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000348055441 none CC(C)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 27, 19, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 5, 27, 27, 26, 27, 27, 27, 27, 21, 21, 19, 19, 5, 5, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348055441 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 Building ZINC000348055441 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348055441 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 477) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000348055441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348055441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000348055441 none CC(C)CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 20, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 4, 4, 28, 28, 24, 28, 28, 28, 28, 22, 22, 20, 20, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 478) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000348055441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348055441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000348055441 none CC(C)CCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 21, 27, 19, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 5, 5, 27, 27, 26, 27, 27, 27, 27, 21, 21, 19, 19, 5, 5, 5, 5, 5, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348055441 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348055441 Building ZINC000348131704 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348131704 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/479 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)cn1) `ZINC000348131704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348131704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348131704 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)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.3', 'F', 'F', 'C.ar', 'Cl', 'C.2', 'N.2', '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, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 5, 5, 5, 5, 5, 14, 14, 5, 5, 6, 6, 12, 12, 12, 12, 12, 6, 2, 5, 5, 5, 14, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/480 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)cn1) `ZINC000348131704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348131704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348131704 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)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.3', 'F', 'F', 'C.ar', 'Cl', 'C.2', 'N.2', '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, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 5, 5, 5, 5, 5, 14, 14, 5, 5, 6, 6, 12, 12, 12, 12, 12, 6, 2, 5, 5, 5, 14, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348131704 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 Building ZINC000348131704 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348131704 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 479) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)cn1) `ZINC000348131704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348131704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348131704 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)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.3', 'F', 'F', 'C.ar', 'Cl', 'C.2', 'N.2', '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, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 5, 5, 5, 5, 5, 14, 14, 5, 5, 6, 6, 12, 12, 12, 12, 12, 6, 2, 5, 5, 5, 14, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 480) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)cn1) `ZINC000348131704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348131704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000348131704 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(F)F)c2Cl)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.3', 'F', 'F', 'C.ar', 'Cl', 'C.2', 'N.2', '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, 5, 15, 15, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 5, 5, 5, 5, 5, 14, 14, 5, 5, 6, 6, 12, 12, 12, 12, 12, 6, 2, 5, 5, 5, 14, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348131704 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348131704 Building ZINC000348135756 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348135756 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/481 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(F)c1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000348135756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348135756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348135756 none O=C(Nc1cc(F)cc(F)c1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 4, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 4, 15, 11, 9, 16, 16, 9, 16, 16, 9] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/482 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(F)c1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000348135756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348135756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348135756 none O=C(Nc1cc(F)cc(F)c1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 5, 15, 15, 15, 15, 1, 1, 1, 8, 8, 8, 8, 15, 15, 8, 15, 15, 8, 4, 15, 14, 8, 15, 15, 8, 15, 15, 8] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348135756 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 Building ZINC000348135756 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348135756 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 481) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(F)c1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000348135756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348135756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348135756 none O=C(Nc1cc(F)cc(F)c1F)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 4, 15, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 4, 15, 11, 9, 16, 16, 9, 16, 16, 9] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 482) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)cc(F)c1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000348135756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348135756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348135756 none O=C(Nc1cc(F)cc(F)c1F)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 15, 1, 1, 15, 1, 15, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 15, 15, 5, 15, 15, 15, 15, 1, 1, 1, 8, 8, 8, 8, 15, 15, 8, 15, 15, 8, 4, 15, 14, 8, 15, 15, 8, 15, 15, 8] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348135756 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348135756 Building ZINC000348141846 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348141846 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/483 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/483' -> `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)Nc1cccc(C(F)F)c1Cl) `ZINC000348141846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348141846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348141846 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 25, 25, 9, 25, 25, 47, 47, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 21, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/484 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/484' -> `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)Nc1cccc(C(F)F)c1Cl) `ZINC000348141846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348141846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348141846 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 6, 23, 23, 45, 45, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 14, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348141846 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 Building ZINC000348141846 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348141846 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 483) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)F)c1Cl) `ZINC000348141846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348141846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348141846 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 25, 25, 9, 25, 25, 47, 47, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 21, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 484) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)F)c1Cl) `ZINC000348141846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348141846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348141846 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)F)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 23, 23, 6, 23, 23, 45, 45, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 23, 23, 14, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348141846 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348141846 Building ZINC000348113453 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348113453 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/485 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348113453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113453 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 11, 11, 19, 19, 11, 11, 11, 11, 6, 6, 6, 12, 12, 12, 6, 6, 4, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/486 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348113453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113453 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 15, 8, 8, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 4, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348113453 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 Building ZINC000348113453 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348113453 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 485) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348113453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113453 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 11, 11, 19, 19, 11, 11, 11, 11, 6, 6, 6, 12, 12, 12, 6, 6, 4, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 486) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348113453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113453 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 15, 8, 8, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 4, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348113453 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113453 Building ZINC000348113454 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348113454 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/487 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348113454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113454 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 15, 8, 8, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 4, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/488 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348113454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113454 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 11, 11, 19, 19, 11, 11, 11, 11, 6, 6, 6, 12, 12, 12, 6, 6, 4, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348113454 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 Building ZINC000348113454 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348113454 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 487) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348113454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113454 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 15, 15, 8, 8, 8, 8, 6, 6, 6, 14, 14, 14, 6, 6, 4, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 488) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl) `ZINC000348113454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348113454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000348113454 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C(C)C)C(F)(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 11, 11, 19, 19, 11, 11, 11, 11, 6, 6, 6, 12, 12, 12, 6, 6, 4, 19, 19, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348113454 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348113454 Building ZINC000293589603 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293589603 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/489 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl) `ZINC000293589603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293589603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589603 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 14, 14, 14, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/490 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl) `ZINC000293589603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293589603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293589603 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 Building ZINC000293589603 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293589603 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 489) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl) `ZINC000293589603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293589603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589603 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 14, 14, 14, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 490) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl) `ZINC000293589603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293589603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589603 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C)[C@@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293589603 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589603 Building ZINC000293589608 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293589608 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/491 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl) `ZINC000293589608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293589608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589608 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/492 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl) `ZINC000293589608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293589608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 14, 14, 14, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293589608 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 Building ZINC000293589608 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293589608 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 491) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl) `ZINC000293589608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293589608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589608 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 2, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 492) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl) `ZINC000293589608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293589608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000293589608 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C)[C@H](C2)C3(F)F)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 14, 14, 14, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293589608 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293589608 Building ZINC000348203617 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348203617 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/493 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O) `ZINC000348203617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348203617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC000348203617 none Cc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 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, 23, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 23, 23, 25, 25, 25, 25, 23, 23, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 50] 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]) total number of confs: 163 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/494 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O) `ZINC000348203617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348203617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC000348203617 none Cc1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 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, 21, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 21, 21, 25, 25, 25, 25, 21, 21, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 50] 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]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348203617 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 Building ZINC000348203617 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348203617 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 493) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O) `ZINC000348203617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348203617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC000348203617 none Cc1cc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 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, 23, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 23, 23, 25, 25, 25, 25, 23, 23, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 50] 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]) total number of confs: 163 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 494) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O) `ZINC000348203617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348203617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC000348203617 none Cc1cc(CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(C)c1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 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, 21, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 21, 21, 25, 25, 25, 25, 21, 21, 12, 12, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 50] 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]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348203617 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348203617 Building ZINC000348192592 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348192592 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/495 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348192592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348192592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348192592 none CCCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 12, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 33, 33, 33, 33, 33, 24, 24, 5, 5, 5, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/496 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348192592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348192592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348192592 none CCCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 5, 5, 5, 4, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 31, 31, 31, 31, 31, 22, 22, 5, 5, 5, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348192592 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 Building ZINC000348192592 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348192592 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 495) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348192592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348192592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348192592 none CCCOc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 12, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 33, 33, 33, 33, 33, 24, 24, 5, 5, 5, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 496) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348192592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348192592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348192592 none CCCOc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 5, 5, 5, 4, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 31, 31, 31, 31, 31, 22, 22, 5, 5, 5, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348192592 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348192592 Building ZINC000193198080 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193198080 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/497 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193198080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193198080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000193198080 none O=C(Nc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 12, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 23, 23, 12, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/498 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193198080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193198080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000193198080 none O=C(Nc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 12, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 23, 23, 19, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193198080 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 Building ZINC000193198080 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193198080 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 497) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193198080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193198080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000193198080 none O=C(Nc1nccn1c1ccccc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 12, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 23, 23, 12, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 498) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193198080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193198080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000193198080 none O=C(Nc1nccn1c1ccccc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 12, 12, 23, 23, 12, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 23, 23, 19, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193198080 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193198080 Building ZINC000348254989 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348254989 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/499 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000348254989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348254989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000348254989 none COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 28, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 28, 28, 28, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/500 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000348254989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348254989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000348254989 none COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 29, 29, 29, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348254989 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 Building ZINC000348254989 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348254989 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 499) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000348254989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348254989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000348254989 none COC(=O)c1sc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 28, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 28, 28, 28, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 500) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C) `ZINC000348254989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348254989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000348254989 none COC(=O)c1sc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 11, 29, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 29, 29, 29, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348254989 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348254989 Building ZINC000348284355 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348284355 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/501 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348284355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284355 none Cc1ccc(C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 6, 14, 14, 3, 6, 1, 3, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 25, 25, 25, 25, 25, 25, 25, 22, 22, 14, 14, 14, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/502 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348284355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284355 none Cc1ccc(C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 21, 11, 4, 11, 11, 3, 4, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 23, 23, 23, 23, 23, 23, 23, 21, 21, 11, 11, 11, 4, 4, 4, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348284355 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 Building ZINC000348284355 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348284355 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 501) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348284355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284355 none Cc1ccc(C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 6, 14, 14, 3, 6, 1, 3, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 25, 25, 25, 25, 25, 25, 25, 22, 22, 14, 14, 14, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 502) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348284355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284355 none Cc1ccc(C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 21, 11, 4, 11, 11, 3, 4, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 23, 23, 23, 23, 23, 23, 23, 21, 21, 11, 11, 11, 4, 4, 4, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348284355 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284355 Building ZINC000348284356 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348284356 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/503 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348284356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284356 none Cc1ccc(C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 24, 13, 5, 13, 13, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 27, 27, 27, 27, 27, 27, 27, 24, 24, 13, 13, 13, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/504 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348284356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284356 none Cc1ccc(C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 13, 5, 13, 13, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 23, 23, 23, 23, 23, 23, 23, 22, 22, 13, 13, 13, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348284356 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 Building ZINC000348284356 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348284356 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 503) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348284356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284356 none Cc1ccc(C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 24, 13, 5, 13, 13, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 27, 27, 27, 27, 27, 27, 27, 24, 24, 13, 13, 13, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 504) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348284356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348284356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348284356 none Cc1ccc(C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 13, 5, 13, 13, 3, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 23, 23, 23, 23, 23, 23, 23, 22, 22, 13, 13, 13, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348284356 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348284356 Building ZINC000348280676 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348280676 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/505 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/506 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/507 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/507' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 26, 26, 26, 18, 26, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 27, 27, 27, 26, 26, 26, 26, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/508 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/508' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 28, 28, 28, 28, 18, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 30, 30, 30, 28, 28, 28, 28, 16, 16, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348280676 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 Building ZINC000348280676 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348280676 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 505) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 506) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 507) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 26, 26, 26, 18, 26, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 27, 27, 27, 26, 26, 26, 26, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 508) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 28, 28, 28, 28, 18, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 30, 30, 30, 28, 28, 28, 28, 16, 16, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348280676 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 Building ZINC000348280676 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348280676 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 505) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 506) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 507) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 26, 26, 26, 18, 26, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 27, 27, 27, 26, 26, 26, 26, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 508) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 28, 28, 28, 28, 18, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 30, 30, 30, 28, 28, 28, 28, 16, 16, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348280676 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 Building ZINC000348280676 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348280676 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 505) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 506) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 18, 27, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 29, 29, 29, 27, 27, 27, 27, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 507) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 26, 26, 26, 26, 18, 26, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 27, 27, 27, 26, 26, 26, 26, 16, 16, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 508) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000348280676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348280676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348280676 none CO[C@H]1CC[C@@H](CCNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 28, 28, 28, 28, 18, 28, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 30, 30, 30, 28, 28, 28, 28, 16, 16, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348280676 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348280676 Building ZINC000348281294 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281294 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/509 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCO[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281294 none O=C(N[C@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 31, 31, 31, 31, 31, 31, 31, 50, 50, 31, 50, 50, 50, 31, 1, 1, 1, 4, 4, 1, 2, 4, 4, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/510 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCO[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281294 none O=C(N[C@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 34, 34, 34, 34, 34, 34, 34, 50, 50, 34, 50, 50, 50, 34, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281294 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 Building ZINC000348281294 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281294 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 509) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCO[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281294 none O=C(N[C@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 31, 31, 31, 31, 31, 31, 31, 50, 50, 31, 50, 50, 50, 31, 1, 1, 1, 4, 4, 1, 2, 4, 4, 5, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 510) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCO[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281294 none O=C(N[C@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 34, 34, 34, 34, 34, 34, 34, 50, 50, 34, 50, 50, 50, 34, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 34, 34, 34, 34, 50, 50, 50, 50, 34, 34, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281294 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281294 Building ZINC000348281296 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281296 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/511 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281296 none O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 31, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 50, 50, 37, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 37, 37, 37, 37, 50, 50, 50, 50, 37, 37, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/512 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281296 none O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 32, 36, 36, 36, 36, 36, 36, 50, 50, 37, 37, 50, 50, 36, 1, 1, 1, 4, 4, 1, 4, 4, 4, 5, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281296 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 Building ZINC000348281296 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281296 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 511) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281296 none O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 31, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 50, 50, 37, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 37, 37, 37, 37, 50, 50, 50, 50, 37, 37, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 512) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281296 none O=C(N[C@@H]1CCO[C@@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 8, 32, 36, 36, 36, 36, 36, 36, 50, 50, 37, 37, 50, 50, 36, 1, 1, 1, 4, 4, 1, 4, 4, 4, 5, 36, 36, 36, 36, 50, 50, 50, 50, 36, 36, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281296 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281296 Building ZINC000348281297 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281297 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/513 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCO[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281297 none O=C(N[C@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 11, 35, 35, 35, 35, 35, 35, 35, 50, 50, 38, 38, 50, 50, 35, 1, 1, 1, 5, 5, 2, 2, 5, 5, 5, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/514 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCO[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281297 none O=C(N[C@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 35, 35, 35, 35, 35, 35, 35, 49, 49, 37, 37, 49, 49, 35, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 35, 35, 35, 35, 49, 49, 49, 49, 35, 35, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281297 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 Building ZINC000348281297 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281297 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 513) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCO[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281297 none O=C(N[C@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 11, 35, 35, 35, 35, 35, 35, 35, 50, 50, 38, 38, 50, 50, 35, 1, 1, 1, 5, 5, 2, 2, 5, 5, 5, 35, 35, 35, 35, 50, 50, 50, 50, 35, 35, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 514) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCO[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281297 none O=C(N[C@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 35, 35, 35, 35, 35, 35, 35, 49, 49, 37, 37, 49, 49, 35, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 35, 35, 35, 35, 49, 49, 49, 49, 35, 35, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281297 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281297 Building ZINC000348281298 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281298 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/515 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281298 none O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 6, 33, 33, 33, 33, 33, 33, 33, 50, 50, 37, 37, 50, 50, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/516 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281298 none O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 30, 30, 30, 30, 30, 30, 30, 49, 49, 33, 33, 49, 49, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 30, 30, 30, 30, 49, 49, 49, 49, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281298 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 Building ZINC000348281298 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348281298 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 515) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348281298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281298 none O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 6, 33, 33, 33, 33, 33, 33, 33, 50, 50, 37, 37, 50, 50, 33, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 33, 33, 33, 33, 50, 50, 50, 50, 33, 33, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 516) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348281298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348281298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348281298 none O=C(N[C@@H]1CCO[C@H](c2ccc(F)cc2)C1)[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', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 30, 30, 30, 30, 30, 30, 30, 49, 49, 33, 33, 49, 49, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 30, 30, 30, 30, 49, 49, 49, 49, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348281298 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348281298 Building ZINC000348311524 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348311524 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/517 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348311524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311524 none Cc1ccc([C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 27, 13, 27, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 13, 13, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/518 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348311524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311524 none Cc1ccc([C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 28, 28, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348311524 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 Building ZINC000348311524 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348311524 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 517) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348311524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311524 none Cc1ccc([C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 27, 13, 27, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 13, 13, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 518) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348311524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311524 none Cc1ccc([C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 28, 28, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348311524 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311524 Building ZINC000348311526 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348311526 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/519 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348311526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311526 none Cc1ccc([C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 12, 29, 29, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 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/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/520 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348311526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311526 none Cc1ccc([C@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 27, 13, 27, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 13, 13, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348311526 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 Building ZINC000348311526 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348311526 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 519) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348311526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311526 none Cc1ccc([C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 12, 29, 29, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 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/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 520) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000348311526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348311526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348311526 none Cc1ccc([C@H](C)CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 27, 13, 27, 27, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 28, 28, 28, 28, 28, 28, 28, 27, 27, 27, 13, 13, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348311526 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348311526 Building ZINC000293788310 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293788310 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/521 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293788310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788310 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 37, 37, 37, 37, 37, 37, 37, 6, 6, 12, 6, 6] 100 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]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/522 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293788310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788310 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 19, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 40, 40, 40, 40, 40, 40, 40, 6, 6, 12, 6, 6] 100 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293788310 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 Building ZINC000293788310 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293788310 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 521) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293788310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788310 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 37, 37, 37, 37, 37, 37, 37, 6, 6, 12, 6, 6] 100 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]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 522) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293788310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788310 none O=C(N[C@@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 19, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 40, 40, 40, 40, 40, 40, 40, 6, 6, 12, 6, 6] 100 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293788310 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788310 Building ZINC000293788313 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293788313 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/523 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293788313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788313 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 39, 39, 39, 39, 39, 39, 39, 6, 6, 12, 6, 6] 100 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/524 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293788313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788313 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 37, 37, 37, 37, 37, 37, 37, 6, 6, 12, 6, 6] 100 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293788313 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 Building ZINC000293788313 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000293788313 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 523) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000293788313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788313 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 39, 39, 39, 39, 39, 39, 39, 6, 6, 12, 6, 6] 100 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 524) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000293788313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000293788313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000293788313 none O=C(N[C@H]1CCCc2sc(Cl)cc21)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 14, 1, 16, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 37, 37, 37, 37, 37, 37, 37, 6, 6, 12, 6, 6] 100 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000293788313 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000293788313 Building ZINC000074393876 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074393876 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/525 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074393876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074393876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074393876 none CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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: [12, 6, 12, 37, 48, 48, 41, 48, 48, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 3, 12, 12, 12, 37, 37, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 188 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/526 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074393876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074393876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074393876 none CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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: [12, 6, 12, 36, 47, 47, 36, 47, 47, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 3, 12, 12, 12, 36, 36, 47, 47, 36, 47, 47, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074393876 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 Building ZINC000074393876 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074393876 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 525) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074393876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074393876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074393876 none CN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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: [12, 6, 12, 37, 48, 48, 41, 48, 48, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 3, 12, 12, 12, 37, 37, 48, 48, 48, 48, 48, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 188 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 526) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074393876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074393876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074393876 none CN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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: [12, 6, 12, 36, 47, 47, 36, 47, 47, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 3, 12, 12, 12, 36, 36, 47, 47, 36, 47, 47, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074393876 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074393876 Building ZINC000074394244 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394244 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/527 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000074394244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394244 none COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 38, 38, 38, 25, 25, 25, 6, 5, 5, 5, 5, 25] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/528 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000074394244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394244 none COc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 38, 38, 38, 25, 25, 25, 6, 5, 5, 5, 5, 25] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394244 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 Building ZINC000074394244 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394244 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 527) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000074394244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394244 none COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 38, 38, 38, 25, 25, 25, 6, 5, 5, 5, 5, 25] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 528) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1) `ZINC000074394244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394244 none COc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 38, 38, 38, 25, 25, 25, 6, 5, 5, 5, 5, 25] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394244 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394244 Building ZINC000074394266 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394266 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/529 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074394266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394266 none COc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 42, 42, 42, 34, 34, 34, 34, 8, 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]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/530 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074394266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394266 none COc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 20, 34, 34, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 42, 42, 42, 34, 34, 34, 34, 8, 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]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394266 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 Building ZINC000074394266 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394266 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 529) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074394266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394266 none COc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 6, 6, 6, 42, 42, 42, 34, 34, 34, 34, 8, 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]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 530) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074394266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394266 none COc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 20, 34, 34, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 42, 42, 42, 34, 34, 34, 34, 8, 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]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394266 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394266 Building ZINC000074394406 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394406 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/531 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000074394406 none CN(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 36, 11, 21, 21, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 21, 21, 36, 36, 36, 36, 36, 36, 21, 21, 11, 6, 6, 6, 6, 21, 21] 42 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/532 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000074394406 none CN(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 35, 18, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 19, 19, 35, 35, 35, 35, 35, 35, 19, 19, 11, 6, 6, 6, 6, 19, 19] 41 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394406 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 Building ZINC000074394406 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394406 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 531) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000074394406 none CN(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [36, 17, 36, 11, 21, 21, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 21, 21, 36, 36, 36, 36, 36, 36, 21, 21, 11, 6, 6, 6, 6, 21, 21] 42 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 532) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000074394406 none CN(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 35, 18, 19, 19, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 19, 19, 35, 35, 35, 35, 35, 35, 19, 19, 11, 6, 6, 6, 6, 19, 19] 41 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394406 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394406 Building ZINC000074394486 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394486 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/533 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394486 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 33, 19, 36, 36, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 11, 6, 6, 6, 6, 36, 36] 46 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/534 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394486 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 36, 33, 36, 36, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 36, 36, 36, 36, 36, 36, 36, 11, 6, 6, 6, 6, 36, 36] 46 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394486 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 Building ZINC000074394486 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074394486 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 533) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074394486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394486 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 33, 19, 36, 36, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 11, 6, 6, 6, 6, 36, 36] 46 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 534) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1) `ZINC000074394486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074394486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC000074394486 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 36, 33, 36, 36, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 1, 6, 6, 36, 36, 36, 36, 36, 36, 36, 11, 6, 6, 6, 6, 36, 36] 46 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074394486 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074394486 Building ZINC000074395945 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074395945 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/535 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074395945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074395945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074395945 none O=C(N1CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4] 12 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/536 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074395945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074395945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074395945 none O=C(N1CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 14 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074395945 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 Building ZINC000074395945 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074395945 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 535) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074395945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074395945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074395945 none O=C(N1CCc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4] 12 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 536) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074395945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074395945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074395945 none O=C(N1CCc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 14 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074395945 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074395945 Building ZINC000074397127 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074397127 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/537 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074397127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074397127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074397127 none O=C(NCc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 27, 44, 44, 27, 44, 44, 44, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 27, 27, 44, 44, 44, 44, 5, 5, 5, 5] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 211 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/538 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074397127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074397127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074397127 none O=C(NCc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 26, 44, 44, 26, 44, 44, 44, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 26, 26, 44, 44, 44, 44, 5, 5, 5, 5] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074397127 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 Building ZINC000074397127 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074397127 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 537) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074397127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074397127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074397127 none O=C(NCc1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 27, 44, 44, 27, 44, 44, 44, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 27, 27, 44, 44, 44, 44, 5, 5, 5, 5] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 211 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 538) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074397127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074397127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074397127 none O=C(NCc1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 26, 44, 44, 26, 44, 44, 44, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 26, 26, 44, 44, 44, 44, 5, 5, 5, 5] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074397127 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397127 Building ZINC000074397824 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074397824 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/539 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074397824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074397824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074397824 none Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 8, 8, 1, 8, 1, 1, 1, 5, 5, 1, 5, 5, 5, 14, 14, 14, 14, 14, 8, 5, 5, 5, 5] 16 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/540 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074397824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074397824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074397824 none Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 8, 8, 1, 8, 1, 1, 1, 5, 5, 1, 4, 5, 5, 14, 14, 14, 14, 14, 8, 5, 5, 5, 5] 16 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074397824 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 Building ZINC000074397824 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074397824 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 539) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074397824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074397824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074397824 none Cc1cnc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 8, 8, 1, 8, 1, 1, 1, 5, 5, 1, 5, 5, 5, 14, 14, 14, 14, 14, 8, 5, 5, 5, 5] 16 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 540) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074397824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074397824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074397824 none Cc1cnc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 14, 8, 8, 1, 8, 1, 1, 1, 5, 5, 1, 4, 5, 5, 14, 14, 14, 14, 14, 8, 5, 5, 5, 5] 16 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074397824 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074397824 Building ZINC000074398232 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074398232 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/541 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074398232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074398232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074398232 none O=C(NCc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 43, 47, 32, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/542 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074398232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074398232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074398232 none O=C(NCc1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 46, 46, 32, 46, 46, 46, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 20, 20, 46, 46, 46, 46, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074398232 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 Building ZINC000074398232 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074398232 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 541) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074398232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074398232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074398232 none O=C(NCc1ccccc1F)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 43, 47, 32, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 542) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074398232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074398232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074398232 none O=C(NCc1ccccc1F)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 20, 46, 46, 32, 46, 46, 46, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 20, 20, 46, 46, 46, 46, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074398232 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074398232 Building ZINC000074400103 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074400103 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/543 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074400103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074400103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074400103 none O=C(NCCc1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 30, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 19, 19, 30, 30, 46, 46, 46, 3, 3, 3, 3] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/544 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cccs1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074400103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074400103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074400103 none O=C(NCCc1cccs1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 30, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 18, 18, 30, 30, 46, 46, 46, 3, 3, 3, 3] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074400103 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 Building ZINC000074400103 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074400103 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 543) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCCc1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074400103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074400103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074400103 none O=C(NCCc1cccs1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 19, 30, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 19, 19, 30, 30, 46, 46, 46, 3, 3, 3, 3] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 544) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCCc1cccs1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074400103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074400103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074400103 none O=C(NCCc1cccs1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 14, 5, 12, 1, 1, 1, 1, 17, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 18, 30, 46, 46, 46, 46, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 18, 18, 30, 30, 46, 46, 46, 3, 3, 3, 3] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074400103 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074400103 Building ZINC000348397047 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348397047 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/545 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348397047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397047 none Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 19, 43, 5, 12, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 43, 43, 43, 43, 43, 43, 12, 12, 12, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43] 47 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/546 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348397047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397047 none Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 19, 45, 5, 11, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 45, 45, 45, 45, 45, 45, 11, 11, 11, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348397047 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 Building ZINC000348397047 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348397047 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 545) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348397047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397047 none Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 19, 43, 5, 12, 1, 5, 1, 1, 1, 5, 5, 1, 2, 5, 5, 43, 43, 43, 43, 43, 43, 12, 12, 12, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43] 47 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 546) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348397047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397047 none Cc1nc2c(s1)[C@@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 19, 45, 5, 11, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 45, 45, 45, 45, 45, 45, 11, 11, 11, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348397047 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397047 Building ZINC000348397049 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348397049 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/547 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348397049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397049 none Cc1nc2c(s1)[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 18, 45, 5, 11, 1, 5, 1, 1, 1, 5, 5, 2, 2, 5, 5, 45, 45, 45, 45, 45, 45, 11, 11, 11, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 125 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/548 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c(s1)[C@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348397049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397049 none Cc1nc2c(s1)[C@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 43, 43, 19, 43, 5, 12, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 43, 43, 43, 43, 43, 43, 12, 12, 12, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43] 48 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348397049 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 Building ZINC000348397049 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348397049 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 547) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc2c(s1)[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348397049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397049 none Cc1nc2c(s1)[C@H](N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 45, 45, 45, 45, 45, 18, 45, 5, 11, 1, 5, 1, 1, 1, 5, 5, 2, 2, 5, 5, 45, 45, 45, 45, 45, 45, 11, 11, 11, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45] 49 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 125 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 548) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc2c(s1)[C@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2) `ZINC000348397049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348397049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000348397049 none Cc1nc2c(s1)[C@H](N(C)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 43, 43, 43, 43, 43, 19, 43, 5, 12, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 43, 43, 43, 43, 43, 43, 12, 12, 12, 5, 5, 5, 5, 43, 43, 43, 43, 43, 43] 48 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 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: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348397049 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348397049 Building ZINC000348406913 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348406913 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/549 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348406913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406913 none Cn1cccc1[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 32, 23, 1, 23, 1, 1, 1, 4, 4, 1, 4, 4, 4, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/550 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348406913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406913 none Cn1cccc1[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 19, 1, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348406913 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 Building ZINC000348406913 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348406913 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 549) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348406913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406913 none Cn1cccc1[C@@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 32, 23, 1, 23, 1, 1, 1, 4, 4, 1, 4, 4, 4, 48, 48, 48, 48, 48, 48, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 550) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348406913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406913 none Cn1cccc1[C@@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 25, 25, 25, 25, 25, 25, 25, 25, 19, 1, 19, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348406913 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406913 Building ZINC000348406916 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348406916 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/551 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348406916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406916 none Cn1cccc1[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 21, 1, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/552 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348406916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406916 none Cn1cccc1[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 23, 1, 25, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348406916 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 Building ZINC000348406916 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348406916 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 551) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348406916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406916 none Cn1cccc1[C@H]1CCCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 21, 1, 22, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 552) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348406916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348406916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000348406916 none Cn1cccc1[C@H]1CCCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 23, 1, 25, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348406916 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348406916 Building ZINC000348409810 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348409810 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/553 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000348409810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348409810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348409810 none CC(C)NC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 43, 43, 20, 12, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/554 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000348409810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348409810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348409810 none CC(C)NC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 36, 26, 35, 4, 4, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 48, 48, 48, 48, 48, 48, 48, 36, 27, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348409810 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 Building ZINC000348409810 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348409810 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 553) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)NC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000348409810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348409810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348409810 none CC(C)NC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 43, 43, 20, 12, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 554) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)NC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1) `ZINC000348409810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348409810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348409810 none CC(C)NC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 36, 26, 35, 4, 4, 20, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 48, 48, 48, 48, 48, 48, 48, 36, 27, 20, 20, 4, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348409810 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348409810 Building ZINC000348426144 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348426144 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/555 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccccc1OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348426144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348426144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000348426144 none CC(C)c1ccccc1OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 50, 30, 11, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 39, 50, 50, 11, 11, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/556 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccccc1OCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348426144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348426144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000348426144 none CC(C)c1ccccc1OCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 30, 11, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 41, 50, 50, 11, 11, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348426144 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 Building ZINC000348426144 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348426144 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 555) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)c1ccccc1OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348426144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348426144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000348426144 none CC(C)c1ccccc1OCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 50, 30, 11, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 39, 50, 50, 11, 11, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 556) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)c1ccccc1OCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348426144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348426144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000348426144 none CC(C)c1ccccc1OCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 30, 11, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 41, 50, 50, 11, 11, 8, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348426144 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348426144 Building ZINC000348431469 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431469 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/557 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/558 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/559 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/559' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/560 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/560' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431469 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 Building ZINC000348431469 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431469 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 557) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 558) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 559) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 560) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431469 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 Building ZINC000348431469 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431469 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 557) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 558) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 559) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 560) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431469 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 Building ZINC000348431469 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431469 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 557) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 558) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 27, 11, 26, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 27, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 559) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 560) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431469 none CC[C@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431469 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431469 Building ZINC000348431470 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431470 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/561 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/562 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/563 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/563' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/564 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/564' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431470 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 Building ZINC000348431470 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431470 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 561) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 562) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 563) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 564) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431470 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 Building ZINC000348431470 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431470 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 561) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 562) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 563) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 564) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431470 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 Building ZINC000348431470 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000348431470 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 561) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 562) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 48, 29, 13, 29, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 29, 29, 29, 29, 29, 29, 13, 13, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 563) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 564) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC000348431470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000348431470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000348431470 none CC[C@@H]1CCCN(C(C)(C)CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 46, 28, 11, 28, 27, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 28, 11, 11, 2, 2, 2, 2, 2, 49, 49] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348431470 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348431470 Building ZINC000074429661 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074429661 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/565 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)nc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074429661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074429661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074429661 none O=C(Nc1ccc(Cl)nc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 8, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 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: [10, 1, 10, 10, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 1, 6, 6, 6, 10, 34, 34, 34, 6, 6, 6, 6] 42 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/566 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)nc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074429661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074429661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074429661 none O=C(Nc1ccc(Cl)nc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 8, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 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: [10, 1, 10, 10, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 1, 6, 6, 6, 10, 34, 34, 34, 6, 6, 6, 6] 42 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074429661 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 Building ZINC000074429661 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074429661 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 565) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)nc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074429661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074429661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074429661 none O=C(Nc1ccc(Cl)nc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 8, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 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: [10, 1, 10, 10, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 1, 6, 6, 6, 10, 34, 34, 34, 6, 6, 6, 6] 42 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 566) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)nc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074429661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074429661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC000074429661 none O=C(Nc1ccc(Cl)nc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 8, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 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: [10, 1, 10, 10, 34, 34, 34, 34, 34, 34, 1, 1, 1, 6, 6, 1, 6, 6, 6, 10, 34, 34, 34, 6, 6, 6, 6] 42 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074429661 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074429661 Building ZINC000074433570 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074433570 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/567 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]ncc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074433570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074433570 none O=C(Nc1ccc2[nH]ncc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 40, 40, 40, 40, 6, 6, 6, 6] 45 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/568 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]ncc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074433570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074433570 none O=C(Nc1ccc2[nH]ncc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 40, 40, 40, 40, 6, 6, 6, 6] 45 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074433570 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 Building ZINC000074433570 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074433570 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 567) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]ncc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074433570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074433570 none O=C(Nc1ccc2[nH]ncc2c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 40, 40, 40, 40, 6, 6, 6, 6] 45 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 568) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]ncc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074433570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074433570 none O=C(Nc1ccc2[nH]ncc2c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 11, 40, 40, 40, 40, 6, 6, 6, 6] 45 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074433570 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433570 Building ZINC000074433915 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074433915 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/569 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074433915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074433915 none O=C(NCc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 49, 49, 49, 49, 49, 48, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/570 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074433915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074433915 none O=C(NCc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074433915 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 Building ZINC000074433915 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074433915 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 569) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074433915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074433915 none O=C(NCc1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 49, 49, 49, 49, 49, 48, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 570) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074433915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074433915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000074433915 none O=C(NCc1cccc(F)c1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 15, 15, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074433915 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074433915 Building ZINC000348444268 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348444268 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/571 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl) `ZINC000348444268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348444268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000348444268 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 32, 32, 20, 32, 32, 32, 32, 32, 10, 10, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 32, 32] 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/572 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl) `ZINC000348444268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348444268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000348444268 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 32, 32] 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348444268 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 Building ZINC000348444268 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348444268 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 571) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl) `ZINC000348444268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348444268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000348444268 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 32, 32, 20, 32, 32, 32, 32, 32, 10, 10, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 32, 32] 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: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 572) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl) `ZINC000348444268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348444268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000348444268 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)ccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 32, 32] 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348444268 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348444268 Building ZINC000348468189 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348468189 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/573 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348468189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468189 none Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 19, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 19, 19, 8, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/574 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348468189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468189 none Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 17, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 17, 17, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348468189 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 Building ZINC000348468189 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348468189 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 573) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348468189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468189 none Cc1ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 19, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 19, 19, 8, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 574) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348468189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468189 none Cc1ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 17, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 17, 17, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348468189 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468189 Building ZINC000348468190 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348468190 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/575 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348468190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468190 none Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 16, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 16, 16, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/576 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348468190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468190 none Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 18, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 18, 18, 8, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348468190 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 Building ZINC000348468190 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348468190 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 575) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348468190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468190 none Cc1ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 16, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 16, 16, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 576) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1) `ZINC000348468190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348468190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000348468190 none Cc1ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 18, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 18, 18, 8, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348468190 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348468190 Building ZINC000074467352 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074467352 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/577 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074467352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074467352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074467352 none CCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 19, 19, 19, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 19, 19, 19, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/578 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074467352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074467352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074467352 none CCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 18, 18, 18, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074467352 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 Building ZINC000074467352 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074467352 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 577) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074467352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074467352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074467352 none CCOc1ncccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 19, 19, 19, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 49, 49, 49, 49, 19, 19, 19, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 578) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074467352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074467352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074467352 none CCOc1ncccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 49, 49, 18, 18, 18, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074467352 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074467352 Building ZINC000074481213 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074481213 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/579 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074481213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074481213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC000074481213 none Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/580 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074481213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074481213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC000074481213 none Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074481213 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 Building ZINC000074481213 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074481213 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 579) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074481213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074481213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC000074481213 none Cc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 580) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1) `ZINC000074481213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074481213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC000074481213 none Cc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074481213 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074481213 Building ZINC000348481840 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348481840 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/581 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348481840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481840 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 7, 16, 16, 11, 16, 16, 16, 16, 10, 10, 10, 10, 10, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/582 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348481840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481840 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 8, 16, 16, 10, 16, 16, 16, 16, 12, 12, 12, 12, 12, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348481840 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 Building ZINC000348481840 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348481840 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 581) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348481840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481840 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 7, 16, 16, 11, 16, 16, 16, 16, 10, 10, 10, 10, 10, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 582) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348481840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481840 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 8, 16, 16, 10, 16, 16, 16, 16, 12, 12, 12, 12, 12, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348481840 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481840 Building ZINC000348481841 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348481841 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/583 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348481841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481841 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 8, 16, 16, 11, 16, 16, 16, 16, 12, 12, 12, 12, 12, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/584 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348481841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481841 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 8, 16, 16, 12, 16, 16, 16, 16, 11, 11, 11, 11, 11, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348481841 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 Building ZINC000348481841 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348481841 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 583) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348481841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481841 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 8, 16, 16, 11, 16, 16, 16, 16, 12, 12, 12, 12, 12, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 584) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F) `ZINC000348481841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348481841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348481841 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 8, 16, 16, 12, 16, 16, 16, 16, 11, 11, 11, 11, 11, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 16, 16, 16] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348481841 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348481841 Building ZINC000074462735 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074462735 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/585 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074462735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074462735 none CN(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 35, 45, 35, 35, 23, 35, 35, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 3, 6, 6, 45, 45, 45, 45, 45, 45, 35, 35, 35, 35, 11, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/586 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074462735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074462735 none CN(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 33, 43, 33, 33, 21, 33, 33, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 6, 6, 6, 43, 43, 43, 43, 43, 43, 33, 33, 33, 33, 9, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074462735 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 Building ZINC000074462735 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074462735 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 585) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074462735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074462735 none CN(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 35, 45, 35, 35, 23, 35, 35, 11, 11, 1, 11, 1, 1, 1, 6, 6, 1, 3, 6, 6, 45, 45, 45, 45, 45, 45, 35, 35, 35, 35, 11, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 586) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074462735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074462735 none CN(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 33, 43, 33, 33, 21, 33, 33, 9, 9, 1, 9, 1, 1, 1, 6, 6, 1, 6, 6, 6, 43, 43, 43, 43, 43, 43, 33, 33, 33, 33, 9, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074462735 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462735 Building ZINC000074462893 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074462893 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/587 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074462893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074462893 none O=C(N1CCOc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/588 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074462893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074462893 none O=C(N1CCOc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074462893 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 Building ZINC000074462893 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074462893 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 587) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074462893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074462893 none O=C(N1CCOc2ccccc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 588) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074462893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074462893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074462893 none O=C(N1CCOc2ccccc21)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074462893 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074462893 Building ZINC000074463358 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074463358 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/589 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074463358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074463358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074463358 none CCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 11, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 16, 18, 18, 4, 4, 4, 4] 28 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/590 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074463358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074463358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074463358 none CCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 11, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 16, 18, 18, 4, 4, 4, 4] 29 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074463358 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 Building ZINC000074463358 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074463358 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 589) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074463358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074463358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074463358 none CCN(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 11, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 16, 18, 18, 4, 4, 4, 4] 28 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 590) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074463358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074463358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074463358 none CCN(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 11, 18, 18, 18, 18, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 16, 16, 16, 16, 16, 18, 18, 4, 4, 4, 4] 29 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074463358 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463358 Building ZINC000074463480 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074463480 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/591 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074463480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463480 none C[C@@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 26, 43, 43, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 29, 29, 26, 26, 26, 43, 43, 43, 43, 43, 3, 3, 3, 3, 29, 29, 29, 29, 29] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/592 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074463480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463480 none C[C@@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 4, 15, 27, 27, 28, 28, 28, 43, 43, 43, 43, 43, 4, 4, 4, 4, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074463480 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 Building ZINC000074463480 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074463480 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 591) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074463480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463480 none C[C@@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 26, 43, 43, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 29, 29, 26, 26, 26, 43, 43, 43, 43, 43, 3, 3, 3, 3, 29, 29, 29, 29, 29] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 592) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074463480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463480 none C[C@@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 4, 15, 27, 27, 28, 28, 28, 43, 43, 43, 43, 43, 4, 4, 4, 4, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074463480 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463480 Building ZINC000074463481 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074463481 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/593 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074463481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463481 none C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 32, 39, 39, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 16, 29, 29, 32, 32, 32, 39, 39, 39, 39, 39, 4, 4, 4, 4, 29, 29, 29, 29, 29] 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]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/594 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074463481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463481 none C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 35, 35, 40, 40, 6, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 33, 33, 35, 35, 35, 40, 40, 40, 40, 40, 3, 3, 3, 3, 33, 33, 33, 33, 33] 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]) total number of confs: 213 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074463481 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 Building ZINC000074463481 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074463481 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 593) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074463481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463481 none C[C@H](C1CC1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 32, 39, 39, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 16, 29, 29, 32, 32, 32, 39, 39, 39, 39, 39, 4, 4, 4, 4, 29, 29, 29, 29, 29] 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]) total number of confs: 194 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 594) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1) `ZINC000074463481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074463481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000074463481 none C[C@H](C1CC1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 35, 35, 40, 40, 6, 1, 6, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 33, 33, 35, 35, 35, 40, 40, 40, 40, 40, 3, 3, 3, 3, 33, 33, 33, 33, 33] 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]) total number of confs: 213 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074463481 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074463481 Building ZINC000074506356 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074506356 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/595 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/595' -> `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)[C@H](C)c1cc(C)ccc1C) `ZINC000074506356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074506356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506356 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 38, 38, 38, 42, 42, 42, 38, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 38, 38, 38, 42, 42, 42, 42, 38, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/596 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/596' -> `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)[C@H](C)c1cc(C)ccc1C) `ZINC000074506356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074506356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506356 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 42, 42, 42, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 42, 42, 42, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074506356 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 Building ZINC000074506356 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074506356 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 595) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cc(C)ccc1C) `ZINC000074506356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074506356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506356 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 38, 38, 38, 42, 42, 42, 38, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 38, 38, 38, 42, 42, 42, 42, 38, 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, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 596) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cc(C)ccc1C) `ZINC000074506356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074506356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506356 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 42, 42, 42, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 42, 42, 42, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074506356 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506356 Building ZINC000074506358 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074506358 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/597 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/597' -> `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)[C@@H](C)c1cc(C)ccc1C) `ZINC000074506358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074506358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506358 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 41, 41, 41, 43, 43, 43, 41, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 41, 41, 41, 43, 43, 43, 43, 41, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/598 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/598' -> `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)[C@@H](C)c1cc(C)ccc1C) `ZINC000074506358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074506358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506358 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 39, 39, 39, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 39, 39, 39, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074506358 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 Building ZINC000074506358 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074506358 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 597) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cc(C)ccc1C) `ZINC000074506358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074506358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506358 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 41, 41, 41, 43, 43, 43, 41, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 41, 41, 41, 43, 43, 43, 43, 41, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 598) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cc(C)ccc1C) `ZINC000074506358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074506358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000074506358 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c1cc(C)ccc1C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 39, 39, 39, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 39, 39, 39, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074506358 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074506358 Building ZINC000074507504 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074507504 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/599 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1) `ZINC000074507504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074507504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074507504 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 15, 22, 22, 22, 22, 22, 22, 15, 15, 15, 6, 6, 6, 6, 22, 22, 22, 22] 30 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/600 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1) `ZINC000074507504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074507504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074507504 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 16, 23, 23, 23, 23, 23, 23, 16, 16, 16, 6, 6, 6, 6, 23, 23, 23, 23] 30 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074507504 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 Building ZINC000074507504 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074507504 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 599) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1) `ZINC000074507504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074507504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074507504 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 15, 22, 22, 22, 22, 22, 22, 15, 15, 15, 6, 6, 6, 6, 22, 22, 22, 22] 30 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 600) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1) `ZINC000074507504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074507504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074507504 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 16, 23, 23, 23, 23, 23, 23, 16, 16, 16, 6, 6, 6, 6, 23, 23, 23, 23] 30 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074507504 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074507504 Building ZINC000074513314 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513314 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/601 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513314 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 34, 34, 34, 34, 34, 43, 43, 39, 43, 43, 1, 1, 1, 5, 5, 1, 2, 5, 5, 10, 34, 34, 43, 43, 43, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/602 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513314 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 31, 31, 42, 42, 39, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 31, 31, 42, 42, 42, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513314 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 Building ZINC000074513314 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513314 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 601) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513314 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 34, 34, 34, 34, 34, 43, 43, 39, 43, 43, 1, 1, 1, 5, 5, 1, 2, 5, 5, 10, 34, 34, 43, 43, 43, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 602) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513314 none O=C(N[C@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 31, 31, 42, 42, 39, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 31, 31, 42, 42, 42, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513314 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513314 Building ZINC000074513315 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513315 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/603 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513315 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 25, 25, 25, 25, 25, 42, 42, 25, 42, 42, 1, 1, 1, 6, 6, 1, 6, 6, 6, 7, 25, 25, 42, 42, 25, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/604 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513315 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 45, 45, 26, 45, 45, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 26, 26, 45, 45, 26, 45, 45, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513315 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 Building ZINC000074513315 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513315 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 603) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513315 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 25, 25, 25, 25, 25, 42, 42, 25, 42, 42, 1, 1, 1, 6, 6, 1, 6, 6, 6, 7, 25, 25, 42, 42, 25, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 604) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513315 none O=C(N[C@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 45, 45, 26, 45, 45, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 26, 26, 45, 45, 26, 45, 45, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513315 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513315 Building ZINC000074513316 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513316 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/605 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513316 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 39, 39, 22, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 22, 22, 39, 39, 22, 39, 39, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/606 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513316 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 25, 25, 41, 41, 25, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 25, 25, 41, 41, 25, 41, 41, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513316 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 Building ZINC000074513316 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513316 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 605) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513316 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 22, 22, 22, 22, 39, 39, 22, 39, 39, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 22, 22, 39, 39, 22, 39, 39, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 606) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513316 none O=C(N[C@@H]1C[C@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 25, 25, 25, 25, 25, 41, 41, 25, 41, 41, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 25, 25, 41, 41, 25, 41, 41, 6, 6, 6, 6] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513316 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513316 Building ZINC000074513317 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513317 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/607 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513317 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 31, 31, 42, 42, 34, 42, 42, 1, 1, 1, 5, 5, 2, 5, 5, 5, 10, 31, 31, 42, 42, 35, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 143 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/608 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513317 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 34, 34, 34, 34, 34, 43, 43, 34, 43, 43, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 34, 34, 43, 43, 34, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513317 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 Building ZINC000074513317 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074513317 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 607) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074513317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513317 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 31, 31, 31, 31, 31, 42, 42, 34, 42, 42, 1, 1, 1, 5, 5, 2, 5, 5, 5, 10, 31, 31, 42, 42, 35, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 143 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 608) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074513317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074513317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000074513317 none O=C(N[C@@H]1C[C@@H]1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 34, 34, 34, 34, 34, 43, 43, 34, 43, 43, 1, 1, 1, 5, 5, 1, 1, 5, 5, 10, 34, 34, 43, 43, 34, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074513317 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074513317 Building ZINC000074536469 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074536469 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/609 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(F)cc21)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074536469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074536469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074536469 none O=C(N1CCc2ccc(F)cc21)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/610 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(F)cc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074536469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074536469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074536469 none O=C(N1CCc2ccc(F)cc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074536469 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 Building ZINC000074536469 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074536469 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 609) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccc(F)cc21)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074536469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074536469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074536469 none O=C(N1CCc2ccc(F)cc21)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 1, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 610) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccc(F)cc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074536469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074536469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000074536469 none O=C(N1CCc2ccc(F)cc21)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 14 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074536469 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074536469 Building ZINC000074539040 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074539040 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/611 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1) `ZINC000074539040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074539040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000074539040 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 29, 43, 43, 29, 41, 41, 9, 9, 9, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 41, 41, 41, 41, 41] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/612 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1) `ZINC000074539040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074539040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000074539040 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 30, 46, 46, 30, 44, 44, 11, 11, 11, 2, 2, 2, 2, 30, 46, 46, 46, 46, 46, 44, 44, 44, 44, 44] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074539040 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 Building ZINC000074539040 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074539040 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 611) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1) `ZINC000074539040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074539040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000074539040 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 29, 43, 43, 29, 41, 41, 9, 9, 9, 3, 3, 3, 3, 29, 43, 43, 43, 43, 43, 41, 41, 41, 41, 41] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 612) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1) `ZINC000074539040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074539040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000074539040 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 30, 46, 46, 30, 44, 44, 11, 11, 11, 2, 2, 2, 2, 30, 46, 46, 46, 46, 46, 44, 44, 44, 44, 44] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074539040 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074539040 Building ZINC000074540330 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074540330 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/613 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074540330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074540330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074540330 none CCCN(CC(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 8, 4, 8, 16, 29, 29, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 23, 23, 16, 16, 29, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/614 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074540330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074540330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074540330 none CCCN(CC(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 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: [27, 22, 8, 4, 8, 16, 29, 29, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 27, 27, 27, 27, 27, 22, 22, 16, 16, 29, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074540330 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 Building ZINC000074540330 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074540330 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 613) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(CC(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074540330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074540330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074540330 none CCCN(CC(F)F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 8, 4, 8, 16, 29, 29, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 23, 23, 16, 16, 29, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 614) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCN(CC(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074540330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074540330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000074540330 none CCCN(CC(F)F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 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: [27, 22, 8, 4, 8, 16, 29, 29, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 27, 27, 27, 27, 27, 22, 22, 16, 16, 29, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074540330 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074540330 Building ZINC000074560031 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074560031 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/615 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccoc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074560031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074560031 none CCN(Cc1ccoc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 12, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 3, 6, 15, 36, 36, 36, 36, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 15, 15, 36, 36, 36, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/616 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccoc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074560031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074560031 none CCN(Cc1ccoc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 12, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 3, 6, 15, 35, 35, 35, 35, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 15, 15, 35, 35, 35, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074560031 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 Building ZINC000074560031 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074560031 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 615) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(Cc1ccoc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074560031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074560031 none CCN(Cc1ccoc1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 12, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 3, 6, 15, 36, 36, 36, 36, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 15, 15, 36, 36, 36, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 616) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(Cc1ccoc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074560031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074560031 none CCN(Cc1ccoc1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 12, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 3, 6, 15, 35, 35, 35, 35, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 15, 15, 35, 35, 35, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074560031 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560031 Building ZINC000074560595 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074560595 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/617 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074560595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074560595 none O=C(NC1(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 20, 33, 33, 20, 33, 33, 20, 20, 1, 1, 1, 6, 6, 1, 6, 6, 6, 12, 33, 33, 20, 33, 33, 20, 20, 20, 20, 6, 6, 6, 6] 44 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/618 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074560595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074560595 none O=C(NC1(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 21, 40, 40, 21, 40, 40, 21, 21, 1, 1, 1, 6, 6, 1, 6, 6, 6, 12, 40, 40, 21, 40, 40, 21, 21, 21, 21, 6, 6, 6, 6] 49 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074560595 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 Building ZINC000074560595 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074560595 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 617) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC1(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074560595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074560595 none O=C(NC1(c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 20, 33, 33, 20, 33, 33, 20, 20, 1, 1, 1, 6, 6, 1, 6, 6, 6, 12, 33, 33, 20, 33, 33, 20, 20, 20, 20, 6, 6, 6, 6] 44 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 618) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC1(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074560595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074560595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000074560595 none O=C(NC1(c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 1, 12, 12, 21, 40, 40, 21, 40, 40, 21, 21, 1, 1, 1, 6, 6, 1, 6, 6, 6, 12, 40, 40, 21, 40, 40, 21, 21, 21, 21, 6, 6, 6, 6] 49 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074560595 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074560595 Building ZINC000074527443 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074527443 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/619 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074527443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074527443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074527443 none Cc1ccsc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 43, 43, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/620 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccsc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074527443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074527443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074527443 none Cc1ccsc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 43, 43, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074527443 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 Building ZINC000074527443 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074527443 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 619) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccsc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074527443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074527443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074527443 none Cc1ccsc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 43, 43, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 620) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccsc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074527443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074527443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000074527443 none Cc1ccsc1CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [43, 43, 43, 43, 43, 19, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 43, 43, 43, 43, 43, 19, 19, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074527443 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074527443 Building ZINC000074532212 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074532212 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/621 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074532212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532212 none C[C@@H](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 10, 31, 31, 49, 49, 49, 49, 49, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 49, 49, 49, 49, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/622 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074532212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532212 none C[C@@H](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 27, 27, 49, 49, 49, 49, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 48, 49, 49, 49, 8, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074532212 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 Building ZINC000074532212 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074532212 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 621) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074532212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532212 none C[C@@H](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 10, 31, 31, 49, 49, 49, 49, 49, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 49, 49, 49, 49, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 622) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074532212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532212 none C[C@@H](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 27, 27, 49, 49, 49, 49, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 27, 27, 27, 48, 49, 49, 49, 8, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074532212 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532212 Building ZINC000074532216 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074532216 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/623 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074532216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532216 none C[C@H](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 27, 27, 49, 49, 49, 49, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 27, 27, 27, 48, 49, 49, 49, 8, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/624 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074532216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532216 none C[C@H](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 10, 31, 31, 49, 49, 49, 49, 49, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 49, 49, 49, 49, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074532216 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 Building ZINC000074532216 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074532216 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 623) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074532216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532216 none C[C@H](c1ccccn1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 8, 27, 27, 49, 49, 49, 49, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 27, 27, 27, 48, 49, 49, 49, 8, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 624) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074532216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074532216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074532216 none C[C@H](c1ccccn1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 10, 31, 31, 49, 49, 49, 49, 49, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 49, 49, 49, 49, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074532216 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074532216 Building ZINC000074533526 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533526 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/625 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533526 none C[C@@H](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 10, 41, 41, 50, 50, 50, 50, 50, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 41, 41, 50, 50, 50, 50, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/626 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533526 none C[C@@H](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 9, 36, 36, 46, 46, 36, 46, 46, 5, 9, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 36, 36, 36, 46, 46, 46, 46, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533526 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 Building ZINC000074533526 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533526 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 625) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533526 none C[C@@H](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 10, 41, 41, 50, 50, 50, 50, 50, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 41, 41, 41, 50, 50, 50, 50, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 626) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533526 none C[C@@H](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 9, 36, 36, 46, 46, 36, 46, 46, 5, 9, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 36, 36, 36, 46, 46, 46, 46, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533526 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533526 Building ZINC000074533530 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533530 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/627 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533530 none C[C@H](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 9, 36, 36, 47, 47, 43, 47, 47, 5, 9, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 36, 36, 36, 47, 47, 47, 47, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/628 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533530 none C[C@H](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 9, 40, 40, 49, 49, 48, 49, 49, 4, 9, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 40, 40, 40, 49, 49, 49, 49, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 176 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533530 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 Building ZINC000074533530 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533530 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 627) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533530 none C[C@H](c1ccncc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 9, 36, 36, 47, 47, 43, 47, 47, 5, 9, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 36, 36, 36, 47, 47, 47, 47, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 628) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533530 none C[C@H](c1ccncc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 9, 40, 40, 49, 49, 48, 49, 49, 4, 9, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 40, 40, 40, 49, 49, 49, 49, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 176 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533530 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533530 Building ZINC000074533664 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533664 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/629 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533664 none C[C@@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 23, 50, 50, 50, 50, 50, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/630 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533664 none C[C@@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 48, 48, 48, 48, 48, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 21, 21, 21, 48, 48, 48, 48, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533664 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 Building ZINC000074533664 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533664 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 629) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533664 none C[C@@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 23, 50, 50, 50, 50, 50, 4, 7, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 630) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533664 none C[C@@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 48, 48, 48, 48, 48, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 21, 21, 21, 48, 48, 48, 48, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533664 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533664 Building ZINC000074533667 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533667 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/631 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533667 none C[C@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 48, 48, 48, 48, 48, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 21, 21, 21, 48, 48, 48, 48, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/632 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533667 none C[C@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 24, 50, 50, 50, 50, 50, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 24, 24, 24, 50, 50, 50, 50, 8, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533667 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 Building ZINC000074533667 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074533667 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 631) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074533667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533667 none C[C@H](c1cccnc1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 48, 48, 48, 48, 48, 4, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 21, 21, 21, 48, 48, 48, 48, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 632) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074533667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074533667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000074533667 none C[C@H](c1cccnc1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 24, 50, 50, 50, 50, 50, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 24, 24, 24, 50, 50, 50, 50, 8, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074533667 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074533667 Building ZINC000348577681 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348577681 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/633 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(CN2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348577681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348577681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348577681 none O=C(Nc1nc(CN2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 10, 5, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 39, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/634 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(CN2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348577681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348577681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348577681 none O=C(Nc1nc(CN2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 10, 5, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 39, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348577681 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 Building ZINC000348577681 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348577681 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 633) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(CN2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348577681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348577681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348577681 none O=C(Nc1nc(CN2CCCCC2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 10, 5, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 39, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 634) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(CN2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348577681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348577681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000348577681 none O=C(Nc1nc(CN2CCCCC2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 5, 10, 5, 5, 5, 5, 5, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 39, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348577681 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348577681 Building ZINC000074581962 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074581962 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/635 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1csc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000074581962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074581962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074581962 none CCc1csc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 16, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 16, 39, 39, 39, 39, 39, 16, 8, 6, 6, 6, 6] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/636 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1csc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000074581962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074581962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074581962 none CCc1csc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 15, 38, 38, 38, 38, 38, 15, 8, 6, 6, 6, 6] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074581962 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 Building ZINC000074581962 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074581962 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 635) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1csc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000074581962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074581962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074581962 none CCc1csc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 16, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 16, 39, 39, 39, 39, 39, 16, 8, 6, 6, 6, 6] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 636) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1csc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1) `ZINC000074581962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074581962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000074581962 none CCc1csc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 15, 38, 38, 38, 38, 38, 15, 8, 6, 6, 6, 6] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074581962 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074581962 Building ZINC000485077262 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485077262 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/637 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F) `ZINC000485077262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485077262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000485077262 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 49 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/638 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F) `ZINC000485077262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485077262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000485077262 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15] 17 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000485077262 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 Building ZINC000485077262 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485077262 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 637) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F) `ZINC000485077262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485077262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000485077262 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 49 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 638) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F) `ZINC000485077262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485077262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000485077262 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15] 17 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000485077262 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485077262 Building ZINC000348706835 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348706835 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/639 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348706835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348706835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348706835 none CC(C)NC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 33, 34, 16, 16, 16, 12, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 46, 33, 16, 16, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/640 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348706835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348706835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348706835 none CC(C)NC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 34, 33, 34, 16, 16, 16, 12, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 50, 50, 50, 50, 50, 50, 50, 45, 33, 16, 16, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348706835 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 Building ZINC000348706835 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348706835 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 639) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348706835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348706835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348706835 none CC(C)NC(=O)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 33, 34, 16, 16, 16, 12, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 46, 33, 16, 16, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 640) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348706835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348706835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348706835 none CC(C)NC(=O)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 34, 33, 34, 16, 16, 16, 12, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 50, 50, 50, 50, 50, 50, 50, 45, 33, 16, 16, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348706835 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348706835 Building ZINC000348707786 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348707786 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/641 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/641' -> `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@@H](c2ccccc2)C2CC2)cn1) `ZINC000348707786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348707786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707786 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 19, 19, 25, 25, 19, 25, 25, 19, 19, 19, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 14, 14, 25, 25, 19, 25, 25, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/642 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/642' -> `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@@H](c2ccccc2)C2CC2)cn1) `ZINC000348707786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348707786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707786 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 18, 18, 24, 24, 18, 24, 24, 18, 18, 18, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 3, 13, 13, 24, 24, 18, 24, 24, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348707786 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 Building ZINC000348707786 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348707786 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 641) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2)C2CC2)cn1) `ZINC000348707786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348707786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707786 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 19, 19, 25, 25, 19, 25, 25, 19, 19, 19, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 14, 14, 25, 25, 19, 25, 25, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 642) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2)C2CC2)cn1) `ZINC000348707786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348707786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707786 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 18, 18, 24, 24, 18, 24, 24, 18, 18, 18, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 3, 13, 13, 24, 24, 18, 24, 24, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348707786 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707786 Building ZINC000348707790 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348707790 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/643 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/643' -> `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@H](c2ccccc2)C2CC2)cn1) `ZINC000348707790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348707790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707790 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 23, 23, 20, 23, 23, 20, 23, 23, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 12, 12, 23, 23, 20, 23, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/644 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/644' -> `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@H](c2ccccc2)C2CC2)cn1) `ZINC000348707790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348707790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707790 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 27, 27, 27, 27, 27, 24, 27, 27, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348707790 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 Building ZINC000348707790 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348707790 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 643) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@H](c2ccccc2)C2CC2)cn1) `ZINC000348707790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348707790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707790 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 23, 23, 20, 23, 23, 20, 23, 23, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 12, 12, 23, 23, 20, 23, 23, 23, 23, 23, 23, 23, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 644) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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@H](c2ccccc2)C2CC2)cn1) `ZINC000348707790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348707790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348707790 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2)C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 27, 27, 27, 27, 27, 24, 27, 27, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348707790 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348707790 Building ZINC000348717494 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348717494 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/645 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2nnco2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348717494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348717494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000348717494 none Cc1ccc(c2nnco2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 5, 5, 1, 5, 1, 1, 1, 6, 6, 1, 1, 6, 6, 30, 30, 30, 30, 30, 46, 30, 5, 6, 6, 6, 6] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/646 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(c2nnco2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348717494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348717494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000348717494 none Cc1ccc(c2nnco2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 5, 5, 1, 5, 1, 1, 1, 6, 6, 1, 1, 6, 6, 30, 30, 30, 30, 30, 46, 30, 5, 6, 6, 6, 6] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348717494 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 Building ZINC000348717494 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348717494 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 645) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(c2nnco2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348717494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348717494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000348717494 none Cc1ccc(c2nnco2)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 5, 5, 1, 5, 1, 1, 1, 6, 6, 1, 1, 6, 6, 30, 30, 30, 30, 30, 46, 30, 5, 6, 6, 6, 6] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 646) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(c2nnco2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348717494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348717494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000348717494 none Cc1ccc(c2nnco2)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 5, 5, 1, 5, 1, 1, 1, 6, 6, 1, 1, 6, 6, 30, 30, 30, 30, 30, 46, 30, 5, 6, 6, 6, 6] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348717494 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348717494 Building ZINC000074688477 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074688477 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/647 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074688477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074688477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074688477 none CC(C)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [48, 35, 48, 35, 35, 35, 35, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 35, 35, 13, 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]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/648 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1nccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074688477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074688477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074688477 none CC(C)n1nccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [48, 35, 48, 35, 35, 35, 35, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 35, 35, 13, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074688477 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 Building ZINC000074688477 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000074688477 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 647) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074688477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000074688477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074688477 none CC(C)n1nccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [48, 35, 48, 35, 35, 35, 35, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 35, 35, 13, 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]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 648) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)n1nccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000074688477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000074688477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000074688477 none CC(C)n1nccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 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: [48, 35, 48, 35, 35, 35, 35, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 35, 35, 13, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000074688477 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000074688477 Building ZINC000348810153 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348810153 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/649 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348810153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810153 none COCCC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 37, 17, 11, 7, 2, 7, 7, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 45, 45, 45, 37, 37, 17, 15, 13, 13, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/650 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348810153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810153 none COCCC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 19, 13, 8, 3, 8, 8, 17, 17, 17, 17, 17, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 44, 44, 44, 37, 37, 17, 19, 15, 15, 17, 17, 17, 17, 17, 17, 17, 3, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348810153 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 Building ZINC000348810153 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348810153 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 649) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348810153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810153 none COCCC[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 37, 17, 11, 7, 2, 7, 7, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 45, 45, 45, 37, 37, 17, 15, 13, 13, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 650) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348810153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810153 none COCCC[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 19, 13, 8, 3, 8, 8, 17, 17, 17, 17, 17, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 44, 44, 44, 37, 37, 17, 19, 15, 15, 17, 17, 17, 17, 17, 17, 17, 3, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348810153 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810153 Building ZINC000348810154 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348810154 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/651 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348810154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810154 none COCCC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 19, 13, 8, 3, 8, 8, 17, 17, 17, 17, 17, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 44, 44, 44, 37, 37, 17, 19, 15, 15, 17, 17, 17, 17, 17, 17, 17, 3, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/652 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348810154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810154 none COCCC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 17, 11, 7, 2, 7, 7, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 46, 46, 46, 38, 38, 15, 17, 13, 13, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348810154 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 Building ZINC000348810154 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348810154 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 651) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348810154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810154 none COCCC[C@@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 19, 13, 8, 3, 8, 8, 17, 17, 17, 17, 17, 17, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 44, 44, 44, 37, 37, 17, 19, 15, 15, 17, 17, 17, 17, 17, 17, 17, 3, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 652) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCCC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348810154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348810154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000348810154 none COCCC[C@@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 17, 11, 7, 2, 7, 7, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 46, 46, 46, 38, 38, 15, 17, 13, 13, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348810154 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348810154 Building ZINC000348814400 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348814400 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/653 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348814400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348814400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348814400 none CSc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 10, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 32, 32, 32, 15, 15, 15, 15, 10, 10, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/654 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348814400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348814400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348814400 none CSc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 13, 15, 15, 10, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 31, 31, 31, 15, 15, 15, 15, 10, 10, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348814400 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 Building ZINC000348814400 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348814400 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 653) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348814400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348814400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348814400 none CSc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 15, 15, 15, 10, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 32, 32, 32, 15, 15, 15, 15, 10, 10, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 654) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000348814400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348814400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348814400 none CSc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 13, 15, 15, 10, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 31, 31, 31, 15, 15, 15, 15, 10, 10, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348814400 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348814400 Building ZINC000348872686 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348872686 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/655 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348872686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348872686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348872686 none Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 35, 50, 50, 50, 50, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 36, 50, 50, 50, 50, 50, 50, 16, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/656 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348872686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348872686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348872686 none Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 34, 50, 50, 50, 50, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 15, 15, 15, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348872686 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 Building ZINC000348872686 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348872686 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 655) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348872686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348872686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348872686 none Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 35, 50, 50, 50, 50, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 16, 16, 16, 36, 50, 50, 50, 50, 50, 50, 16, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 656) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000348872686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348872686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000348872686 none Cc1c(NC(=O)N(C)C)cccc1NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 34, 50, 50, 50, 50, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 15, 15, 15, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 142 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348872686 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348872686 Building ZINC000193963218 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193963218 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/657 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2ncccc2c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193963218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193963218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000193963218 none O=C(NCc1ccc2ncccc2c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/658 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2ncccc2c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193963218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193963218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000193963218 none O=C(NCc1ccc2ncccc2c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193963218 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 Building ZINC000193963218 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193963218 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 657) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccc2ncccc2c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193963218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193963218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000193963218 none O=C(NCc1ccc2ncccc2c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 658) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccc2ncccc2c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000193963218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193963218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000193963218 none O=C(NCc1ccc2ncccc2c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193963218 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193963218 Building ZINC000348888006 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348888006 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/659 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/659' -> `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](c3ccccc3)C2)cn1) `ZINC000348888006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348888006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888006 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 6, 10, 15, 15, 15, 15, 15, 15, 21, 21, 18, 21, 21, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 21, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/660 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/660' -> `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](c3ccccc3)C2)cn1) `ZINC000348888006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348888006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888006 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22, 22, 14, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22, 22, 14, 14, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348888006 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 Building ZINC000348888006 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348888006 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 659) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3ccccc3)C2)cn1) `ZINC000348888006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348888006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888006 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 6, 10, 15, 15, 15, 15, 15, 15, 21, 21, 18, 21, 21, 15, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 15, 15, 15, 15, 15, 15, 21, 21, 21, 21, 21, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 660) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3ccccc3)C2)cn1) `ZINC000348888006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348888006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888006 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22, 22, 14, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 14, 14, 14, 14, 14, 14, 22, 22, 22, 22, 22, 14, 14, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348888006 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888006 Building ZINC000348888009 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348888009 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/661 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/661' -> `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](c3ccccc3)C2)cn1) `ZINC000348888009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348888009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888009 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 2, 5, 7, 12, 12, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 12, 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, 48, 49]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/662 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/662' -> `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](c3ccccc3)C2)cn1) `ZINC000348888009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348888009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888009 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 2, 5, 7, 11, 11, 11, 11, 11, 11, 21, 21, 11, 21, 21, 11, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 11, 11, 11, 11, 11, 11, 21, 21, 11, 21, 21, 11, 11, 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, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348888009 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 Building ZINC000348888009 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348888009 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 661) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3ccccc3)C2)cn1) `ZINC000348888009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348888009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888009 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 2, 5, 7, 12, 12, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 12, 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, 48, 49]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 662) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3ccccc3)C2)cn1) `ZINC000348888009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348888009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000348888009 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](c3ccccc3)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.ar', 'C.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', '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, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 2, 5, 7, 11, 11, 11, 11, 11, 11, 21, 21, 11, 21, 21, 11, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 11, 11, 11, 11, 11, 11, 21, 21, 11, 21, 21, 11, 11, 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, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348888009 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348888009 Building ZINC000348956598 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956598 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/663 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956598 none CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 26, 26, 7, 20, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/664 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956598 none CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 29, 29, 29, 29, 8, 19, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 29, 29, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956598 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 Building ZINC000348956598 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956598 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 663) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956598 none CCO[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 26, 26, 7, 20, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 664) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956598 none CCO[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 29, 29, 29, 29, 8, 19, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 49, 49, 49, 49, 49, 29, 29, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956598 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956598 Building ZINC000348956599 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956599 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/665 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956599 none CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 10, 33, 4, 1, 4, 1, 1, 1, 4, 4, 2, 2, 4, 4, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/666 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956599 none CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 11, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956599 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 Building ZINC000348956599 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956599 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 665) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956599 none CCO[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 10, 33, 4, 1, 4, 1, 1, 1, 4, 4, 2, 2, 4, 4, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 666) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956599 none CCO[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 11, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956599 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956599 Building ZINC000348956600 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956600 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/667 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956600 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 11, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/668 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956600 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 32, 32, 9, 32, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 32, 32, 4, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956600 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 Building ZINC000348956600 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956600 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 667) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956600 none CCO[C@@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 11, 33, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 668) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956600 none CCO[C@@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 32, 32, 9, 32, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 32, 32, 4, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956600 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956600 Building ZINC000348956601 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956601 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/669 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956601 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 38, 38, 38, 38, 7, 27, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 38, 4, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/670 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956601 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 9, 25, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956601 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 Building ZINC000348956601 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348956601 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 669) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348956601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956601 none CCO[C@@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 38, 38, 38, 38, 7, 27, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 50, 50, 50, 50, 50, 38, 38, 4, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 670) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2) `ZINC000348956601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348956601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000348956601 none CCO[C@@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C12CCCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 33, 33, 33, 9, 25, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348956601 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348956601 Building ZINC000348966079 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348966079 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/671 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1) `ZINC000348966079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348966079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348966079 none Cc1nc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 4, 5, 5, 26, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 6, 5, 5, 5, 5, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/672 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1) `ZINC000348966079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348966079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348966079 none Cc1nc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 6, 5, 5, 5, 5, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348966079 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 Building ZINC000348966079 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000348966079 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 671) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1) `ZINC000348966079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000348966079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348966079 none Cc1nc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 2, 4, 5, 5, 26, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 6, 5, 5, 5, 5, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 672) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1) `ZINC000348966079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000348966079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000348966079 none Cc1nc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 6, 5, 5, 5, 5, 26] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000348966079 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000348966079 Building ZINC000485608718 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485608718 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/673 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485608718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608718 none O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 27, 44, 44, 49, 49, 44, 49, 49, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 27, 27, 49, 49, 44, 49, 49, 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, 36]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/674 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485608718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608718 none O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 44, 44, 50, 50, 50, 50, 50, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 24, 24, 50, 50, 50, 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, 36]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000485608718 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 Building ZINC000485608718 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485608718 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 673) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485608718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608718 none O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 27, 44, 44, 49, 49, 44, 49, 49, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 27, 27, 49, 49, 44, 49, 49, 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, 36]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 674) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485608718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608718 none O=C(NC[C@@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 44, 44, 50, 50, 50, 50, 50, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 24, 24, 50, 50, 50, 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, 36]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000485608718 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608718 Building ZINC000485608719 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485608719 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/675 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485608719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608719 none O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 44, 44, 50, 50, 44, 50, 50, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 2, 4, 4, 5, 24, 24, 50, 50, 44, 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, 36]) total number of confs: 220 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/676 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485608719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608719 none O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 27, 44, 44, 49, 49, 44, 49, 49, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 27, 27, 49, 49, 44, 49, 49, 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, 36]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000485608719 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 Building ZINC000485608719 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000485608719 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 675) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000485608719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608719 none O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 24, 44, 44, 50, 50, 44, 50, 50, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 2, 4, 4, 5, 24, 24, 50, 50, 44, 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, 36]) total number of confs: 220 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 676) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000485608719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000485608719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000485608719 none O=C(NC[C@H](c1ccccc1)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 27, 44, 44, 49, 49, 44, 49, 49, 44, 44, 44, 44, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 27, 27, 49, 49, 44, 49, 49, 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, 36]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000485608719 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000485608719 Building ZINC000194129176 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194129176 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/677 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194129176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194129176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000194129176 none O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 6, 6, 6, 29, 50, 50, 32, 50, 50, 50, 50, 6, 6, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 6, 6, 6, 6, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/678 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194129176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194129176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000194129176 none O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 5, 5, 5, 24, 50, 50, 24, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 3, 3, 5, 5, 5, 5, 5, 50, 50, 50, 5, 5, 5, 5, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194129176 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 Building ZINC000194129176 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194129176 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 677) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194129176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194129176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000194129176 none O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 6, 6, 6, 29, 50, 50, 32, 50, 50, 50, 50, 6, 6, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 6, 6, 50, 50, 50, 6, 6, 6, 6, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 678) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194129176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194129176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000194129176 none O=C(N1CCC(Oc2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 5, 5, 5, 5, 24, 50, 50, 24, 50, 50, 50, 50, 5, 5, 1, 1, 1, 3, 3, 1, 3, 3, 5, 5, 5, 5, 5, 50, 50, 50, 5, 5, 5, 5, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194129176 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194129176 Building ZINC000349007503 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349007503 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/679 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349007503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007503 none O=C(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 38, 50, 50, 50, 50, 17, 17, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/680 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349007503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007503 none O=C(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 29, 50, 50, 50, 50, 9, 9, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349007503 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 Building ZINC000349007503 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349007503 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 679) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349007503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007503 none O=C(C[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 38, 50, 50, 50, 50, 17, 17, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 680) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349007503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007503 none O=C(C[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 29, 50, 50, 50, 50, 9, 9, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349007503 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007503 Building ZINC000349007504 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349007504 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/681 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349007504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007504 none O=C(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 10, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 10, 10, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/682 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349007504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007504 none O=C(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 37, 50, 50, 50, 50, 16, 16, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349007504 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 Building ZINC000349007504 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349007504 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 681) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349007504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007504 none O=C(C[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 10, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 10, 10, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 682) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1) `ZINC000349007504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349007504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349007504 none O=C(C[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 37, 50, 50, 50, 50, 16, 16, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349007504 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349007504 Building ZINC000349102143 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349102143 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/683 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C) `ZINC000349102143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349102143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000349102143 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 28, 10, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 28, 28, 28, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/684 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C) `ZINC000349102143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349102143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000349102143 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 10, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 27, 27, 27, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349102143 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 Building ZINC000349102143 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349102143 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 683) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C) `ZINC000349102143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349102143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000349102143 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 28, 10, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 28, 28, 28, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 684) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C) `ZINC000349102143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349102143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000349102143 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 10, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 27, 27, 27, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349102143 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349102143 Building ZINC000349085486 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349085486 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/685 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1) `ZINC000349085486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349085486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085486 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 14, 14, 30, 40, 14, 24, 28, 28, 24, 28, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 30, 30, 40, 40, 40, 24, 24, 28, 28, 28, 28, 28] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/686 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1) `ZINC000349085486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349085486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085486 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 19, 19, 36, 41, 19, 26, 28, 28, 26, 28, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 36, 36, 41, 41, 41, 26, 26, 28, 28, 28, 28, 28] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349085486 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 Building ZINC000349085486 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349085486 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 685) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1) `ZINC000349085486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349085486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085486 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 14, 14, 30, 40, 14, 24, 28, 28, 24, 28, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 30, 30, 40, 40, 40, 24, 24, 28, 28, 28, 28, 28] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 686) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1) `ZINC000349085486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349085486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085486 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 19, 19, 36, 41, 19, 26, 28, 28, 26, 28, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 36, 36, 41, 41, 41, 26, 26, 28, 28, 28, 28, 28] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349085486 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085486 Building ZINC000349085487 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349085487 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/687 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000349085487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349085487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085487 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 19, 19, 36, 41, 19, 26, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 36, 36, 41, 41, 41, 26, 26, 28, 28, 28, 28, 28] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/688 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000349085487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349085487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085487 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 15, 15, 31, 41, 15, 25, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 31, 31, 41, 41, 41, 25, 25, 29, 29, 29, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349085487 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 Building ZINC000349085487 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349085487 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 687) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000349085487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349085487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085487 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 19, 19, 36, 41, 19, 26, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 36, 36, 41, 41, 41, 26, 26, 28, 28, 28, 28, 28] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 688) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1) `ZINC000349085487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349085487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000349085487 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)[C@@H](COC)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 7, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 8, 15, 15, 31, 41, 15, 25, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 31, 31, 41, 41, 41, 25, 25, 29, 29, 29, 29, 29] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349085487 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349085487 Building ZINC000349107065 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349107065 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/689 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1) `ZINC000349107065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349107065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000349107065 none CCCCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 20, 7, 7, 2, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/690 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1) `ZINC000349107065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349107065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000349107065 none CCCCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 20, 7, 7, 2, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349107065 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 Building ZINC000349107065 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349107065 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 689) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1) `ZINC000349107065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349107065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000349107065 none CCCCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 20, 7, 7, 2, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 690) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1) `ZINC000349107065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349107065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000349107065 none CCCCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 20, 20, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 20, 7, 7, 2, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349107065 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349107065 Building ZINC000349110507 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110507 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/691 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21) `ZINC000349110507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000349110507 none CC(C)n1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 5, 4, 4, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/692 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21) `ZINC000349110507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000349110507 none CC(C)n1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 5, 5, 5, 5, 5, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110507 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 Building ZINC000349110507 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110507 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 691) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21) `ZINC000349110507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000349110507 none CC(C)n1c(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 5, 4, 4, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 692) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21) `ZINC000349110507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000349110507 none CC(C)n1c(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)nc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', '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', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 5, 5, 5, 5, 5, 49, 49, 49, 49] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 126 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110507 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110507 Building ZINC000349110512 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110512 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/693 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110512 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 35, 35, 20, 1, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/694 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110512 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 15, 2, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 50, 50, 36, 44, 50, 50, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 30, 30, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110512 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 Building ZINC000349110512 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110512 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 693) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110512 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 35, 35, 20, 1, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 35, 35, 50, 50, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 694) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110512 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 15, 2, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 30, 30, 30, 30, 50, 50, 36, 44, 50, 50, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 30, 30, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110512 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110512 Building ZINC000349110513 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110513 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/695 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110513 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 43, 49, 49, 49, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 30, 30, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/696 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110513 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 16, 1, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 36, 36, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 31, 31, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110513 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 Building ZINC000349110513 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110513 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 695) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110513 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 49, 49, 43, 49, 49, 49, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 30, 30, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 696) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1) `ZINC000349110513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110513 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 16, 1, 16, 1, 1, 1, 5, 5, 1, 1, 5, 5, 31, 31, 31, 31, 49, 49, 36, 36, 49, 49, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 31, 31, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110513 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110513 Building ZINC000349110514 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110514 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/697 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110514 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 13, 2, 15, 1, 1, 1, 5, 5, 1, 2, 5, 5, 32, 32, 32, 32, 49, 49, 32, 33, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 5, 5, 32, 32, 49, 49, 49, 49] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/698 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110514 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 11, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 34, 50, 50, 34, 35, 50, 50, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110514 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 Building ZINC000349110514 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110514 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 697) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110514 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 13, 2, 15, 1, 1, 1, 5, 5, 1, 2, 5, 5, 32, 32, 32, 32, 49, 49, 32, 33, 49, 49, 32, 32, 32, 32, 32, 32, 5, 5, 5, 5, 32, 32, 49, 49, 49, 49] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 698) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110514 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 34, 11, 2, 14, 1, 1, 1, 4, 4, 1, 1, 4, 4, 34, 34, 34, 34, 50, 50, 34, 35, 50, 50, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 34, 34, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110514 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110514 Building ZINC000349110515 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110515 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/699 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110515 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 14, 1, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 49, 49, 32, 49, 49, 49, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 32, 32, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/700 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110515 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 49, 49, 29, 49, 49, 49, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 29, 29, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110515 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 Building ZINC000349110515 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349110515 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 699) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349110515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110515 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 14, 1, 14, 1, 1, 1, 6, 6, 1, 1, 6, 6, 32, 32, 32, 32, 49, 49, 32, 49, 49, 49, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 32, 32, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 700) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1) `ZINC000349110515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349110515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000349110515 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C[C@H](c2ccc(F)cc2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 14, 1, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 29, 29, 29, 29, 49, 49, 29, 49, 49, 49, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 29, 29, 49, 49, 49, 49] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349110515 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349110515 Building ZINC000194234340 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194234340 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/701 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194234340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194234340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000194234340 none O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 8, 6, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 34, 34, 34, 50, 50, 34, 34, 34, 17, 1, 1, 1, 3, 3, 1, 3, 3, 4, 17, 17, 17, 50, 50, 50, 50, 50, 17, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/702 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194234340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194234340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000194234340 none O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 8, 6, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 35, 35, 35, 50, 50, 35, 35, 35, 16, 1, 1, 1, 3, 3, 1, 3, 3, 4, 16, 16, 16, 50, 50, 50, 50, 50, 16, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194234340 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 Building ZINC000194234340 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194234340 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 701) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194234340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194234340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000194234340 none O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 8, 6, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 17, 34, 34, 34, 50, 50, 34, 34, 34, 17, 1, 1, 1, 3, 3, 1, 3, 3, 4, 17, 17, 17, 50, 50, 50, 50, 50, 17, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 702) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194234340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194234340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000194234340 none O=C(Nc1cccc(c2nc(C3CC3)n[nH]2)c1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 8, 6, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 16, 16, 16, 16, 35, 35, 35, 50, 50, 35, 35, 35, 16, 1, 1, 1, 3, 3, 1, 3, 3, 4, 16, 16, 16, 50, 50, 50, 50, 50, 16, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194234340 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194234340 Building ZINC000349128365 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349128365 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/703 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349128365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349128365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000349128365 none O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 16, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 45, 45, 11, 45, 45, 45, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 45, 45, 43, 45, 5, 5, 5, 5] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/704 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349128365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349128365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000349128365 none O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 16, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 45, 45, 11, 45, 45, 45, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 45, 45, 41, 45, 5, 5, 5, 5] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349128365 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 Building ZINC000349128365 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349128365 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 703) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349128365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349128365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000349128365 none O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 16, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 45, 45, 11, 45, 45, 45, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 45, 45, 43, 45, 5, 5, 5, 5] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 704) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349128365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349128365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000349128365 none O=C(Nc1n[nH]c(c2ccccc2Cl)n1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 16, 8, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 11, 11, 11, 45, 45, 11, 45, 45, 45, 11, 1, 1, 1, 5, 5, 1, 1, 5, 5, 4, 45, 45, 41, 45, 5, 5, 5, 5] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349128365 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349128365 Building ZINC000349192892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349192892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/705 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/706 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/707 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/707' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/708 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/708' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349192892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 Building ZINC000349192892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349192892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 705) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 706) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 707) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 708) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349192892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 Building ZINC000349192892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349192892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 705) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 706) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 707) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 708) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349192892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 Building ZINC000349192892 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349192892 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 705) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 706) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 8, 28, 25, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 8, 28, 28, 8, 8, 2, 2, 2, 2, 2, 28] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 707) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 708) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000349192892.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349192892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349192892 none CC(C)N(C)Cc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 30, 30, 10, 30, 25, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 10, 30, 30, 10, 10, 2, 2, 2, 2, 2, 30] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349192892 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349192892 Building ZINC000349193678 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349193678 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/709 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349193678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000349193678 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 47, 50, 50, 47, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/710 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349193678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000349193678 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 48, 50, 50, 48, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349193678 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 Building ZINC000349193678 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349193678 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 709) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349193678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000349193678 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 47, 50, 50, 47, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 710) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349193678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000349193678 none CN(Cc1nc2c(s1)CCCC2)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 48, 50, 50, 48, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349193678 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193678 Building ZINC000349193808 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349193808 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/711 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349193808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349193808 none CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 45, 11, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/712 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349193808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349193808 none CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 44, 11, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349193808 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 Building ZINC000349193808 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349193808 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 711) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349193808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349193808 none CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 45, 11, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 712) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000349193808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349193808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349193808 none CC(C)(C)OC(=O)CCC(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 44, 11, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349193808 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349193808 Building ZINC000349194383 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349194383 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/713 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349194383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194383 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 47, 47, 46, 47, 47, 47, 36, 36, 36, 17, 17, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/714 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349194383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194383 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 49, 49, 44, 49, 49, 49, 31, 31, 31, 16, 16, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349194383 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 Building ZINC000349194383 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349194383 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 713) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349194383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194383 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 17, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 47, 47, 46, 47, 47, 47, 36, 36, 36, 17, 17, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 714) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349194383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194383 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 49, 49, 44, 49, 49, 49, 31, 31, 31, 16, 16, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349194383 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194383 Building ZINC000349194386 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349194386 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/715 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349194386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194386 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 49, 49, 43, 49, 49, 49, 31, 31, 31, 16, 16, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/716 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349194386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194386 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 47, 47, 47, 47, 47, 47, 35, 35, 35, 16, 16, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349194386 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 Building ZINC000349194386 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349194386 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 715) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349194386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194386 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 28, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 49, 49, 43, 49, 49, 49, 31, 31, 31, 16, 16, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 716) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1) `ZINC000349194386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349194386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000349194386 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 47, 47, 47, 47, 47, 47, 35, 35, 35, 16, 16, 4, 3, 3, 3, 3, 47, 47, 47, 47] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349194386 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349194386 Building ZINC000194348573 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348573 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/717 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/718 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/719 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/719' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/720 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/720' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348573 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 Building ZINC000194348573 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348573 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 717) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 718) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 719) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 720) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348573 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 Building ZINC000194348573 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348573 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 717) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 718) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 719) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 720) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348573 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 Building ZINC000194348573 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348573 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 717) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 718) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 22, 43, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 43, 43, 43, 50, 50, 50, 50, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 3, 2, 2, 1, 2, 2, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 719) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 720) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348573 none CN1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 23, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348573 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348573 Building ZINC000194348592 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348592 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/721 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/722 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/723 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/723' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/724 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/724' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348592 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 Building ZINC000194348592 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348592 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 721) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 722) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 723) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 724) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348592 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 Building ZINC000194348592 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348592 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 721) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 722) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 723) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 724) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348592 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 Building ZINC000194348592 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000194348592 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 721) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 722) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 17, 35, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 35, 35, 35, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 723) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 724) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1) `ZINC000194348592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000194348592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000194348592 none CN1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccccc2)[C@@H]1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 17, 36, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 36, 36, 36, 50, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 1, 3, 3, 50, 50, 50] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194348592 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194348592 Building ZINC000349286130 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349286130 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/725 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc2ccccc2o1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000349286130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349286130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000349286130 none CN(Cc1cc2ccccc2o1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 15, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 5, 5, 5, 15, 15, 26, 26, 26, 26, 26, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/726 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc2ccccc2o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000349286130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349286130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000349286130 none CN(Cc1cc2ccccc2o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 5, 5, 5, 13, 13, 24, 24, 24, 24, 24, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349286130 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 Building ZINC000349286130 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349286130 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 725) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1cc2ccccc2o1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000349286130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349286130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000349286130 none CN(Cc1cc2ccccc2o1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 15, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 5, 5, 5, 15, 15, 26, 26, 26, 26, 26, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 726) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(Cc1cc2ccccc2o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000349286130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349286130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000349286130 none CN(Cc1cc2ccccc2o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 5, 5, 5, 13, 13, 24, 24, 24, 24, 24, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349286130 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349286130 Building ZINC000349325653 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349325653 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/727 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1) `ZINC000349325653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349325653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349325653 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 42, 42, 34, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 42, 42, 42, 50, 50, 50, 42, 42, 34, 34, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 42] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/728 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1) `ZINC000349325653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349325653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349325653 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 43, 43, 35, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 50, 50, 50, 43, 43, 35, 35, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 43] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349325653 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 Building ZINC000349325653 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349325653 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 727) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1) `ZINC000349325653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349325653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349325653 none COc1ccc(CCNC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 42, 42, 34, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 42, 42, 42, 50, 50, 50, 42, 42, 34, 34, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 42] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 728) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1) `ZINC000349325653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349325653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000349325653 none COc1ccc(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 43, 43, 35, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 43, 43, 43, 50, 50, 50, 43, 43, 35, 35, 17, 17, 4, 3, 3, 3, 3, 3, 3, 3, 43] 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349325653 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349325653 Building ZINC000194512164 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194512164 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/729 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194512164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194512164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194512164 none O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 1, 5, 5, 9, 10, 10, 10, 5, 5, 2, 5, 5] 10 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/730 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194512164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194512164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194512164 none O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 1, 5, 5, 9, 10, 10, 10, 5, 5, 1, 5, 5] 10 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194512164 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 Building ZINC000194512164 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194512164 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 729) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194512164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194512164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194512164 none O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 1, 5, 5, 9, 10, 10, 10, 5, 5, 2, 5, 5] 10 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 730) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194512164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194512164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194512164 none O=C(Nc1nc2cc(C(F)(F)F)ccc2[nH]1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 1, 5, 5, 9, 10, 10, 10, 5, 5, 1, 5, 5] 10 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000194512164 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000194512164 Building ZINC000349433404 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349433404 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/731 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C) `ZINC000349433404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349433404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000349433404 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 23, 4, 7, 22, 22, 22, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 23, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/732 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C) `ZINC000349433404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349433404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000349433404 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 23, 4, 4, 22, 22, 22, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 23, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349433404 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 Building ZINC000349433404 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349433404 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 731) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C) `ZINC000349433404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349433404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000349433404 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 23, 4, 7, 22, 22, 22, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 23, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 732) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C) `ZINC000349433404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349433404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000349433404 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)cc(OC)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 5, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 23, 4, 4, 22, 22, 22, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 23, 23, 23, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349433404 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349433404 Building ZINC000295500809 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295500809 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/733 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1) `ZINC000295500809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295500809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500809 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 2, 12, 15, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/734 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1) `ZINC000295500809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295500809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500809 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 2, 10, 13, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295500809 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 Building ZINC000295500809 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295500809 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 733) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1) `ZINC000295500809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295500809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500809 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 2, 12, 15, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 734) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1) `ZINC000295500809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295500809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500809 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 2, 10, 13, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295500809 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500809 Building ZINC000295500812 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295500812 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/735 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1) `ZINC000295500812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295500812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500812 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 14, 17, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/736 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1) `ZINC000295500812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295500812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500812 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 1, 1, 1, 2, 16, 19, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295500812 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 Building ZINC000295500812 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295500812 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 735) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1) `ZINC000295500812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295500812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500812 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 14, 17, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 736) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1) `ZINC000295500812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295500812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000295500812 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](C)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 1, 1, 1, 2, 16, 19, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 79 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295500812 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295500812 Building ZINC000295604948 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295604948 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/737 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCC(O)CC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000295604948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295604948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000295604948 none O=C(N1CCC2(CCC(O)CC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 24, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 46, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 147, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/738 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CCC(O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000295604948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295604948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000295604948 none O=C(N1CCC2(CCC(O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 27, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295604948 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 Building ZINC000295604948 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295604948 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 737) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC2(CCC(O)CC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000295604948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295604948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000295604948 none O=C(N1CCC2(CCC(O)CC2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 24, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 46, 1, 1, 1, 4, 4, 1, 1, 4, 4, 49, 49, 49, 49, 49, 49, 49, 49, 49, 147, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 738) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC2(CCC(O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000295604948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295604948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000295604948 none O=C(N1CCC2(CCC(O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 27, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 45, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 48, 48, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4] 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295604948 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295604948 Building ZINC000349745798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349745798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/739 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/740 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 36, 50, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 2, 2, 1, 2, 2, 5, 5, 5, 5, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/741 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/741' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/742 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/742' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349745798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 Building ZINC000349745798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349745798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 739) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 740) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 36, 50, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 2, 2, 1, 2, 2, 5, 5, 5, 5, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 741) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 742) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349745798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 Building ZINC000349745798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349745798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 739) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 740) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 36, 50, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 2, 2, 1, 2, 2, 5, 5, 5, 5, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 741) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 742) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349745798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 Building ZINC000349745798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000349745798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 739) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 50, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 2, 2, 4, 4, 4, 4, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 740) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 36, 50, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 2, 2, 1, 2, 2, 5, 5, 5, 5, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 104 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 741) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 742) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1) `ZINC000349745798.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000349745798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000349745798 none C[C@H]1CC[C@@H](OC2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 2, 2, 1, 2, 2, 6, 6, 6, 6, 50, 50, 50, 50] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349745798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349745798 Building ZINC000349804619 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349804619 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/743 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1) `ZINC000349804619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349804619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804619 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 30, 30, 23, 30, 30, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/744 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1) `ZINC000349804619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349804619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804619 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 30, 30, 27, 30, 30, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349804619 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 Building ZINC000349804619 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349804619 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 743) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1) `ZINC000349804619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349804619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804619 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 11, 2, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 30, 30, 23, 30, 30, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 744) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1) `ZINC000349804619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349804619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804619 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 21, 9, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 30, 30, 27, 30, 30, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349804619 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804619 Building ZINC000349804620 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349804620 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/745 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1) `ZINC000349804620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349804620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804620 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 29, 29, 23, 29, 29, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/746 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1) `ZINC000349804620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349804620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804620 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 12, 2, 12, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 29, 29, 29, 36, 36, 31, 36, 36, 29, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349804620 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 Building ZINC000349804620 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349804620 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 745) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1) `ZINC000349804620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349804620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804620 none CC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 10, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 29, 29, 23, 29, 29, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 746) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1) `ZINC000349804620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349804620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000349804620 none CC1(C)CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H]1c1ccncc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 12, 2, 12, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 29, 29, 29, 36, 36, 31, 36, 36, 29, 29, 29, 29, 29, 29, 29, 29, 6, 11, 11, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349804620 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349804620 Building ZINC000295833759 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295833759 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/747 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000295833759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295833759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000295833759 none O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 11, 31, 31, 31, 31, 31, 31, 31, 31, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 31, 31, 31, 31, 31, 31, 31, 31, 49, 49, 5, 5, 10, 5, 5] 100 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: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/748 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000295833759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295833759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000295833759 none O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 11, 34, 34, 34, 34, 34, 34, 34, 34, 49, 49, 49, 49, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 49, 49, 6, 6, 12, 6, 6] 100 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295833759 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 Building ZINC000295833759 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000295833759 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 747) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000295833759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000295833759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000295833759 none O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 11, 31, 31, 31, 31, 31, 31, 31, 31, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 31, 31, 31, 31, 31, 31, 31, 31, 49, 49, 5, 5, 10, 5, 5] 100 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: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 748) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000295833759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000295833759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000295833759 none O=C(N[C@H]1CCCC[C@H]1CC(F)(F)F)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 5, 7, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 11, 34, 34, 34, 34, 34, 34, 34, 34, 49, 49, 49, 49, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 49, 49, 6, 6, 12, 6, 6] 100 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000295833759 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000295833759 Building ZINC000349856854 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349856854 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/749 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000349856854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349856854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000349856854 none Cc1csc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 50, 50, 50, 50, 50, 29, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/750 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000349856854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349856854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000349856854 none Cc1csc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 50, 50, 50, 50, 50, 24, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349856854 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 Building ZINC000349856854 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349856854 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 749) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1csc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000349856854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349856854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000349856854 none Cc1csc(NC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 50, 50, 50, 50, 50, 29, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 750) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1csc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1) `ZINC000349856854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349856854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000349856854 none Cc1csc(NC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 50, 50, 50, 50, 50, 24, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349856854 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349856854 Building ZINC000349858759 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349858759 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/751 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1) `ZINC000349858759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349858759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858759 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 8, 15, 15, 15, 15, 15, 28, 48, 48, 48, 48, 48, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/752 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1) `ZINC000349858759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349858759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858759 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 14, 14, 14, 14, 14, 27, 49, 49, 49, 49, 49, 14, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349858759 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 Building ZINC000349858759 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349858759 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 751) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1) `ZINC000349858759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349858759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858759 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 8, 15, 15, 15, 15, 15, 28, 48, 48, 48, 48, 48, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 752) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1) `ZINC000349858759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349858759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858759 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 14, 14, 14, 14, 14, 27, 49, 49, 49, 49, 49, 14, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349858759 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858759 Building ZINC000349858760 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349858760 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/753 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1) `ZINC000349858760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349858760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858760 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 27, 44, 44, 44, 44, 44, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/754 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1) `ZINC000349858760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349858760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858760 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 17, 17, 17, 17, 17, 30, 49, 49, 49, 49, 49, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349858760 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 Building ZINC000349858760 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349858760 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 753) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1) `ZINC000349858760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349858760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858760 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 27, 44, 44, 44, 44, 44, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 754) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1) `ZINC000349858760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349858760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000349858760 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C2CCCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 17, 17, 17, 17, 17, 30, 49, 49, 49, 49, 49, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349858760 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349858760 Building ZINC000349859795 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349859795 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/755 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349859795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859795 none O=C(N1CCO[C@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 9, 9, 9, 9, 9, 15, 28, 28, 28, 28, 28, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/756 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349859795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859795 none O=C(N1CCO[C@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 6, 8, 8, 8, 8, 8, 14, 27, 27, 27, 27, 27, 8, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349859795 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 Building ZINC000349859795 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349859795 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 755) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCO[C@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859795.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349859795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859795 none O=C(N1CCO[C@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 9, 9, 9, 9, 9, 15, 28, 28, 28, 28, 28, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 756) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCO[C@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859795.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349859795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859795 none O=C(N1CCO[C@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 6, 8, 8, 8, 8, 8, 14, 27, 27, 27, 27, 27, 8, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349859795 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859795 Building ZINC000349859798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349859798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/757 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349859798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859798 none O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 10, 10, 10, 10, 16, 27, 27, 27, 27, 27, 10, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/758 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349859798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859798 none O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 10, 10, 10, 10, 17, 28, 28, 28, 28, 28, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349859798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 Building ZINC000349859798 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000349859798 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 757) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000349859798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859798 none O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 10, 10, 10, 10, 10, 16, 27, 27, 27, 27, 27, 10, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 758) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000349859798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000349859798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000349859798 none O=C(N1CCO[C@@H](C2CCCCC2)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 10, 10, 10, 10, 17, 28, 28, 28, 28, 28, 10, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000349859798 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000349859798 Building ZINC000350028369 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350028369 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/759 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000350028369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350028369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350028369 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 11, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 43, 43, 43, 43, 43, 17, 17, 17, 17] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/760 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000350028369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350028369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350028369 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 14, 14, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 40, 40, 40, 40, 40, 14, 14, 14, 14] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350028369 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 Building ZINC000350028369 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350028369 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 759) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000350028369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350028369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350028369 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 11, 17, 17, 17, 17, 43, 43, 43, 43, 43, 43, 43, 43, 43, 17, 17, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 43, 43, 43, 43, 43, 17, 17, 17, 17] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 760) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1) `ZINC000350028369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350028369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350028369 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ccccc32)CC1 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 14, 14, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 40, 40, 40, 40, 40, 14, 14, 14, 14] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350028369 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350028369 Building ZINC000350018334 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350018334 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/761 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350018334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350018334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018334 none O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 6, 6, 12, 42, 42, 42, 42, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/762 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350018334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350018334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018334 none O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 6, 6, 12, 41, 41, 41, 41, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350018334 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 Building ZINC000350018334 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350018334 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 761) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350018334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350018334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018334 none O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 6, 6, 12, 42, 42, 42, 42, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 762) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350018334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350018334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018334 none O=C(N[C@@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 6, 6, 12, 41, 41, 41, 41, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350018334 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018334 Building ZINC000350018341 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350018341 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/763 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350018341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350018341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018341 none O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 6, 6, 12, 41, 41, 41, 41, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/764 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350018341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350018341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018341 none O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 6, 6, 12, 42, 42, 42, 42, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350018341 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 Building ZINC000350018341 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350018341 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 763) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350018341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350018341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018341 none O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 1, 6, 6, 12, 41, 41, 41, 41, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 764) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350018341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350018341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000350018341 none O=C(N[C@H]1COc2c1ccc(Cl)c2Cl)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 16, 1, 16, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 21, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 6, 6, 1, 6, 6, 12, 42, 42, 42, 42, 6, 6, 1, 6, 6] 47 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350018341 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350018341 Building ZINC000487086582 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487086582 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/765 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21) `ZINC000487086582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487086582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487086582 none CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24] 35 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/766 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21) `ZINC000487086582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487086582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487086582 none CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 29 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487086582 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 Building ZINC000487086582 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487086582 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 765) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21) `ZINC000487086582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487086582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487086582 none CC(C)CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 14, 14, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24] 35 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 766) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21) `ZINC000487086582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487086582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000487086582 none CC(C)CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCCc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 29 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 72 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487086582 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487086582 Building ZINC000350089491 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350089491 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/767 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cccc(C)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000350089491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350089491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350089491 none CSc1cccc(C)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 9, 9, 9, 5, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 24, 24, 24, 9, 9, 9, 9, 9, 9, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/768 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cccc(C)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000350089491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350089491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350089491 none CSc1cccc(C)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 5, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 23, 23, 23, 9, 9, 9, 9, 9, 9, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350089491 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 Building ZINC000350089491 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350089491 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 767) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1cccc(C)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000350089491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350089491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350089491 none CSc1cccc(C)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 9, 9, 9, 5, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 24, 24, 24, 9, 9, 9, 9, 9, 9, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 768) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1cccc(C)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000350089491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350089491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350089491 none CSc1cccc(C)c1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 5, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 23, 23, 23, 9, 9, 9, 9, 9, 9, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350089491 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350089491 Building ZINC000350090879 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350090879 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/769 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1) `ZINC000350090879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350090879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350090879 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 6, 6, 6, 6, 33, 44, 44, 35, 44, 44, 44, 6, 5, 5, 5, 5, 5, 5, 3, 6, 33, 33, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/770 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1) `ZINC000350090879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350090879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350090879 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 33, 44, 44, 33, 42, 44, 44, 6, 4, 4, 4, 4, 4, 4, 3, 6, 33, 33, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350090879 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 Building ZINC000350090879 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350090879 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 769) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1) `ZINC000350090879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350090879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350090879 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 6, 6, 6, 6, 33, 44, 44, 35, 44, 44, 44, 6, 5, 5, 5, 5, 5, 5, 3, 6, 33, 33, 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]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 770) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1) `ZINC000350090879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350090879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350090879 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(F)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 33, 44, 44, 33, 42, 44, 44, 6, 4, 4, 4, 4, 4, 4, 3, 6, 33, 33, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350090879 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350090879 Building ZINC000350100371 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350100371 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/771 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350100371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350100371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000350100371 none O=C(Nc1ccc(CN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 6, 6, 45, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 10, 10, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/772 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350100371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350100371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000350100371 none O=C(Nc1ccc(CN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 4, 6, 42, 50, 50, 50, 50, 11, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 11, 11, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350100371 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 Building ZINC000350100371 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350100371 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 771) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(CN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350100371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350100371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000350100371 none O=C(Nc1ccc(CN2CCCC2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 10, 10, 6, 6, 45, 50, 50, 50, 50, 10, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 10, 10, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 772) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(CN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350100371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350100371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000350100371 none O=C(Nc1ccc(CN2CCCC2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 11, 11, 4, 6, 42, 50, 50, 50, 50, 11, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 11, 11, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350100371 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350100371 Building ZINC000296280855 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280855 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/773 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C) `ZINC000296280855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280855 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31] 49 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/774 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C) `ZINC000296280855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280855 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 1, 7, 7, 1, 1, 1, 2, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280855 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 Building ZINC000296280855 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280855 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 773) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C) `ZINC000296280855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280855 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31] 49 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 774) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C) `ZINC000296280855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280855 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 1, 7, 7, 1, 1, 1, 2, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280855 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280855 Building ZINC000296280862 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280862 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/775 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C) `ZINC000296280862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280862 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 7, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17] 31 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/776 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C) `ZINC000296280862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280862 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21] 38 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280862 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 Building ZINC000296280862 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280862 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 775) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C) `ZINC000296280862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280862 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 7, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17] 31 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 776) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C) `ZINC000296280862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280862 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 2, 9, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21] 38 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280862 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280862 Building ZINC000296280866 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280866 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/777 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280866 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/778 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280866 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 3, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30] 46 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280866 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 Building ZINC000296280866 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280866 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 777) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280866 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 778) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280866 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 3, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30] 46 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280866 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280866 Building ZINC000296280873 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280873 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/779 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280873 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/780 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280873 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19] 32 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280873 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 Building ZINC000296280873 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000296280873 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 779) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000296280873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280873 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20] 33 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 780) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C) `ZINC000296280873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000296280873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000296280873 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19] 32 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000296280873 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000296280873 Building ZINC000350181760 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350181760 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/781 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350181760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350181760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000350181760 none O=C(Nc1ccnn1c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/782 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350181760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350181760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000350181760 none O=C(Nc1ccnn1c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 14, 14, 14, 22, 24, 24, 24, 24, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 14, 14, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350181760 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 Building ZINC000350181760 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350181760 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 781) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350181760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350181760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000350181760 none O=C(Nc1ccnn1c1cccc(F)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 8, 15, 15, 15, 15, 15, 24, 24, 24, 24, 24, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 782) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccnn1c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350181760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350181760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000350181760 none O=C(Nc1ccnn1c1cccc(F)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 14, 14, 14, 22, 24, 24, 24, 24, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 14, 14, 24, 24, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350181760 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350181760 Building ZINC000487410008 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487410008 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/783 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C) `ZINC000487410008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487410008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000487410008 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 19, 19, 19, 30, 49, 49, 30, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 19, 19, 19, 30, 30, 49, 49, 30, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 236 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/784 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C) `ZINC000487410008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487410008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000487410008 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 18, 18, 18, 30, 46, 46, 45, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 18, 18, 18, 30, 30, 46, 46, 45, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 173 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487410008 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 Building ZINC000487410008 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487410008 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 783) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C) `ZINC000487410008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487410008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000487410008 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 19, 19, 19, 30, 49, 49, 30, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 19, 19, 19, 30, 30, 49, 49, 30, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 236 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 784) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C) `ZINC000487410008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487410008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000487410008 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)Cc1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 18, 18, 18, 30, 46, 46, 45, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 18, 18, 18, 30, 30, 46, 46, 45, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 173 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487410008 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487410008 Building ZINC000487431256 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487431256 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/785 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487431256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431256 none Cc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 17, 11, 3, 11, 11, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 29, 17, 17, 11, 11, 11, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/786 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487431256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431256 none Cc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 27, 27, 17, 9, 3, 9, 9, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 27, 27, 27, 27, 17, 27, 27, 17, 17, 9, 9, 9, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487431256 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 Building ZINC000487431256 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487431256 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 785) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487431256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431256 none Cc1ccccc1C[C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 17, 11, 3, 11, 11, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 29, 17, 17, 11, 11, 11, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 786) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487431256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431256 none Cc1ccccc1C[C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 27, 27, 17, 9, 3, 9, 9, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 27, 27, 27, 27, 17, 27, 27, 17, 17, 9, 9, 9, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487431256 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431256 Building ZINC000487431259 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487431259 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/787 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487431259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431259 none Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 17, 10, 3, 10, 10, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 26, 26, 26, 26, 26, 26, 26, 17, 17, 10, 10, 10, 3, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/788 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487431259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431259 none Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 11, 3, 11, 11, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 30, 30, 30, 30, 30, 30, 30, 18, 18, 11, 11, 11, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487431259 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 Building ZINC000487431259 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487431259 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 787) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487431259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431259 none Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 17, 10, 3, 10, 10, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 26, 26, 26, 26, 26, 26, 26, 17, 17, 10, 10, 10, 3, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 788) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000487431259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487431259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000487431259 none Cc1ccccc1C[C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 11, 3, 11, 11, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 30, 30, 30, 30, 30, 30, 30, 18, 18, 11, 11, 11, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000487431259 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000487431259 Building ZINC000350313199 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350313199 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/789 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1) `ZINC000350313199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350313199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350313199 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 47, 47, 47, 47, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/790 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1) `ZINC000350313199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350313199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350313199 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 5, 5, 5, 5, 5, 5, 4, 20, 20, 20, 47, 47, 47, 47, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350313199 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 Building ZINC000350313199 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350313199 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 789) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1) `ZINC000350313199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350313199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350313199 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 47, 47, 47, 47, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 790) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1) `ZINC000350313199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350313199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000350313199 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(c2nc3ccccc3[nH]2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 5, 5, 5, 5, 5, 5, 4, 20, 20, 20, 47, 47, 47, 47, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350313199 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350313199 Building ZINC000577294815 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577294815 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/791 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577294815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294815 none Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 14, 35, 35, 35, 35, 35, 35, 14, 14, 14, 14, 3, 3, 14, 14, 35] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/792 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577294815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294815 none Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 13, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 3, 3, 13, 13, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000577294815 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 Building ZINC000577294815 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577294815 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 791) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577294815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294815 none Cc1ccnc([C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 14, 35, 35, 35, 35, 35, 35, 14, 14, 14, 14, 3, 3, 14, 14, 35] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 792) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577294815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294815 none Cc1ccnc([C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 13, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 3, 3, 13, 13, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000577294815 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294815 Building ZINC000577294817 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577294817 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/793 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577294817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294817 none Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 2, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 3, 3, 14, 14, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/794 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577294817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294817 none Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 35, 35, 14, 14, 14, 14, 4, 4, 14, 14, 35] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000577294817 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 Building ZINC000577294817 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577294817 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 793) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577294817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294817 none Cc1ccnc([C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 2, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 3, 3, 14, 14, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 794) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1) `ZINC000577294817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577294817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000577294817 none Cc1ccnc([C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 35, 35, 35, 35, 35, 35, 14, 14, 14, 14, 4, 4, 14, 14, 35] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000577294817 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577294817 Building ZINC000128347473 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128347473 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/795 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128347473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347473 none CCc1ccc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 26, 26, 26, 26, 26, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/796 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128347473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347473 none CCc1ccc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 29, 29, 29, 29, 29, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000128347473 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 Building ZINC000128347473 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128347473 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 795) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1ccc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128347473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347473 none CCc1ccc([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 26, 26, 26, 26, 26, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 796) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1ccc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128347473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347473 none CCc1ccc([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 29, 29, 29, 29, 29, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000128347473 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347473 Building ZINC000128347714 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128347714 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/797 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128347714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347714 none CCc1ccc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 28, 28, 28, 28, 28, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/798 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128347714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347714 none CCc1ccc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 17, 27, 27, 27, 27, 27, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000128347714 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 Building ZINC000128347714 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000128347714 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 797) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1ccc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000128347714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347714 none CCc1ccc([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 28, 28, 28, 28, 28, 20, 20, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 798) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCc1ccc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1) `ZINC000128347714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000128347714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000128347714 none CCc1ccc([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 17, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 17, 27, 27, 27, 27, 27, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000128347714 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000128347714 Building ZINC000045443473 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000045443473 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/799 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000045443473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443473 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 28, 28, 28, 28, 7, 4, 7, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 28, 48, 47, 47, 47, 28, 28, 7, 7, 7, 4, 3, 3, 3, 3, 3, 3, 3, 28, 48, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/800 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000045443473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443473 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 25, 25, 25, 25, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 47, 46, 46, 46, 25, 25, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 25, 47, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000045443473 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 Building ZINC000045443473 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000045443473 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 799) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000045443473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443473 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 28, 28, 28, 28, 7, 4, 7, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 28, 28, 28, 48, 47, 47, 47, 28, 28, 7, 7, 7, 4, 3, 3, 3, 3, 3, 3, 3, 28, 48, 48, 48] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 800) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000045443473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443473 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 25, 25, 25, 25, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 47, 46, 46, 46, 25, 25, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 25, 47, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000045443473 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443473 Building ZINC000045443474 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000045443474 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/801 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000045443474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443474 none COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 25, 25, 25, 25, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 25, 25, 25, 47, 46, 46, 46, 25, 25, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 25, 47, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/802 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000045443474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443474 none COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 28, 28, 28, 28, 7, 4, 7, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 49, 47, 47, 47, 28, 28, 7, 7, 7, 4, 3, 3, 3, 3, 3, 3, 3, 28, 49, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000045443474 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 Building ZINC000045443474 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000045443474 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 801) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000045443474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443474 none COc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 25, 25, 25, 25, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 25, 25, 25, 47, 46, 46, 46, 25, 25, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 25, 47, 47, 47] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 802) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC) `ZINC000045443474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000045443474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000045443474 none COc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 28, 28, 28, 28, 7, 4, 7, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 49, 47, 47, 47, 28, 28, 7, 7, 7, 4, 3, 3, 3, 3, 3, 3, 3, 28, 49, 49, 49] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000045443474 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000045443474 Building ZINC000192572018 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192572018 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/803 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192572018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572018 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 6, 14, 14, 6, 14, 14, 14, 32, 32, 32, 18, 18, 3, 3, 3, 6, 6, 6, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/804 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192572018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572018 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 7, 15, 15, 7, 7, 15, 15, 36, 36, 36, 24, 24, 4, 3, 3, 6, 6, 6, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192572018 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 Building ZINC000192572018 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192572018 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 803) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192572018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572018 none COC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 6, 14, 14, 6, 14, 14, 14, 32, 32, 32, 18, 18, 3, 3, 3, 6, 6, 6, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 804) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192572018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572018 none COC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 7, 15, 15, 7, 7, 15, 15, 36, 36, 36, 24, 24, 4, 3, 3, 6, 6, 6, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192572018 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572018 Building ZINC000192572029 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192572029 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/805 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192572029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572029 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 7, 15, 15, 15, 15, 15, 15, 37, 37, 37, 24, 24, 4, 3, 3, 6, 6, 6, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/806 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192572029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572029 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 6, 14, 14, 6, 6, 14, 14, 32, 32, 32, 18, 18, 3, 3, 3, 6, 6, 6, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192572029 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 Building ZINC000192572029 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192572029 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 805) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192572029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572029 none COC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 7, 15, 15, 15, 15, 15, 15, 37, 37, 37, 24, 24, 4, 3, 3, 6, 6, 6, 3, 3, 15, 15, 15, 15] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 144 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 806) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1) `ZINC000192572029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192572029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000192572029 none COC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 16, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 6, 14, 14, 6, 6, 14, 14, 32, 32, 32, 18, 18, 3, 3, 3, 6, 6, 6, 3, 3, 14, 14, 14, 14] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192572029 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192572029 Building ZINC000192992256 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192992256 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/807 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1) `ZINC000192992256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192992256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000192992256 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 19, 40, 40, 40, 40, 11, 11, 9, 9, 9, 9, 9, 9, 9, 5, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/808 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1) `ZINC000192992256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192992256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000192992256 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 9, 9, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 20, 38, 38, 38, 38, 12, 12, 9, 9, 9, 9, 9, 9, 9, 5, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 12, 12, 12, 9, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192992256 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 Building ZINC000192992256 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000192992256 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 807) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1) `ZINC000192992256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000192992256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000192992256 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 19, 40, 40, 40, 40, 11, 11, 9, 9, 9, 9, 9, 9, 9, 5, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 808) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1) `ZINC000192992256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000192992256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000192992256 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cnn(C3CCCC3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 9, 9, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 20, 38, 38, 38, 38, 12, 12, 9, 9, 9, 9, 9, 9, 9, 5, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 12, 12, 12, 9, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000192992256 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000192992256 Building ZINC000193000352 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193000352 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/809 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000193000352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193000352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000193000352 none CCCNc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 7, 26, 26, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 26, 26, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 7, 7, 2, 2, 2, 3, 3, 3, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/810 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000193000352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193000352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000193000352 none CCCNc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 7, 7, 26, 26, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 26, 26, 50, 50, 50, 50, 50, 36, 36, 35, 26, 26, 7, 7, 2, 2, 2, 3, 3, 3, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193000352 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 Building ZINC000193000352 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193000352 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 809) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCNc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000193000352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193000352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000193000352 none CCCNc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 7, 26, 26, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 26, 26, 50, 50, 50, 50, 50, 34, 34, 34, 26, 26, 7, 7, 2, 2, 2, 3, 3, 3, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 810) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCNc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1) `ZINC000193000352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193000352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000193000352 none CCCNc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 7, 7, 26, 26, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 2, 2, 26, 26, 50, 50, 50, 50, 50, 36, 36, 35, 26, 26, 7, 7, 2, 2, 2, 3, 3, 3, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193000352 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193000352 Building ZINC000577519827 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577519827 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/811 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1) `ZINC000577519827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577519827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000577519827 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 14, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 48, 48, 48, 48, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/812 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1) `ZINC000577519827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577519827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000577519827 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 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, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000577519827 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 Building ZINC000577519827 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000577519827 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 811) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1) `ZINC000577519827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000577519827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000577519827 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 14, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 22, 22, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 48, 48, 48, 48, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 812) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1) `ZINC000577519827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000577519827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000577519827 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 23, 23, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 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, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000577519827 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000577519827 Building ZINC000193453230 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193453230 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/813 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C) `ZINC000193453230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193453230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000193453230 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 8, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/814 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C) `ZINC000193453230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193453230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000193453230 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 14, 14, 7, 14, 14, 4, 4, 4, 8, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193453230 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 Building ZINC000193453230 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000193453230 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 813) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C) `ZINC000193453230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000193453230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000193453230 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 8, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 814) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C) `ZINC000193453230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000193453230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000193453230 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 14, 14, 7, 14, 14, 4, 4, 4, 8, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000193453230 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000193453230 Building ZINC000350642184 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350642184 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/815 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350642184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642184 none Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 5, 9, 9, 24, 48, 48, 48, 48, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 48, 48, 48, 5, 4, 4, 1, 4, 4, 17, 17, 17, 17] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/816 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350642184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642184 none Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 19, 19, 10, 6, 10, 10, 22, 48, 48, 48, 48, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 48, 48, 48, 6, 4, 4, 1, 4, 4, 19, 19, 19, 19] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350642184 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 Building ZINC000350642184 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350642184 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 815) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350642184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642184 none Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 5, 9, 9, 24, 48, 48, 48, 48, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 48, 48, 48, 5, 4, 4, 1, 4, 4, 17, 17, 17, 17] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 816) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350642184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642184 none Cc1ccc([C@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 19, 19, 10, 6, 10, 10, 22, 48, 48, 48, 48, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 48, 48, 48, 6, 4, 4, 1, 4, 4, 19, 19, 19, 19] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350642184 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642184 Building ZINC000350642185 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350642185 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/817 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350642185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642185 none Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 19, 19, 10, 6, 10, 10, 22, 48, 48, 48, 48, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 48, 48, 48, 6, 4, 4, 1, 4, 4, 19, 19, 19, 19] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/818 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350642185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642185 none Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 24, 48, 48, 48, 48, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 48, 48, 48, 5, 4, 4, 1, 4, 4, 17, 17, 17, 17] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350642185 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 Building ZINC000350642185 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350642185 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 817) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350642185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642185 none Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 19, 19, 10, 6, 10, 10, 22, 48, 48, 48, 48, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 48, 48, 48, 6, 4, 4, 1, 4, 4, 19, 19, 19, 19] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 237 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 818) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1) `ZINC000350642185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350642185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350642185 none Cc1ccc([C@@H](Cn2ccnc2)NC(=O)[C@]([O-])([SiH3])c2ccccc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 24, 48, 48, 48, 48, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 48, 48, 48, 5, 4, 4, 1, 4, 4, 17, 17, 17, 17] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350642185 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350642185 Building ZINC000350694604 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350694604 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/819 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS[C@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350694604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694604 none CCS[C@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 10, 10, 10, 10, 10, 10, 10, 4, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/820 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS[C@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350694604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694604 none CCS[C@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 6, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350694604 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 Building ZINC000350694604 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350694604 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 819) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCS[C@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350694604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694604 none CCS[C@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 10, 10, 10, 10, 10, 10, 10, 4, 2, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 820) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCS[C@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350694604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694604 none CCS[C@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 6, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350694604 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694604 Building ZINC000350694606 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350694606 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/821 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS[C@@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350694606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694606 none CCS[C@@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/822 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS[C@@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350694606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694606 none CCS[C@@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 12, 12, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 12, 26, 26, 26, 26, 26, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350694606 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 Building ZINC000350694606 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350694606 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 821) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCS[C@@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350694606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694606 none CCS[C@@H]1CCCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 822) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCS[C@@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1) `ZINC000350694606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350694606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000350694606 none CCS[C@@H]1CCCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 12, 12, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 12, 26, 26, 26, 26, 26, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350694606 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350694606 Building ZINC000350699899 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350699899 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/823 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350699899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350699899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699899 none O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 9, 9, 9, 9, 9, 40, 40, 40, 40, 40, 50, 50, 50, 50, 50, 40, 1, 1, 1, 2, 2, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/824 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350699899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350699899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699899 none O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 50, 50, 41, 50, 50, 41, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 6, 6, 6, 50, 50, 41, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350699899 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 Building ZINC000350699899 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350699899 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 823) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350699899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350699899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699899 none O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 9, 9, 9, 9, 9, 40, 40, 40, 40, 40, 50, 50, 50, 50, 50, 40, 1, 1, 1, 2, 2, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 824) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350699899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350699899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699899 none O=C(N1CCC[C@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 6, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 50, 50, 41, 50, 50, 41, 1, 1, 1, 2, 2, 1, 2, 2, 6, 6, 6, 6, 6, 6, 50, 50, 41, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350699899 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699899 Building ZINC000350699900 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350699900 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/825 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350699900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350699900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699900 none O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 42, 42, 42, 42, 42, 50, 50, 42, 50, 50, 42, 1, 1, 1, 2, 2, 1, 2, 2, 7, 7, 7, 7, 7, 7, 50, 50, 42, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/826 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350699900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350699900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699900 none O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 9, 9, 9, 9, 9, 41, 41, 41, 41, 41, 50, 50, 42, 50, 50, 41, 1, 1, 1, 2, 2, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 46, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350699900 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 Building ZINC000350699900 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350699900 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 825) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350699900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350699900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699900 none O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 42, 42, 42, 42, 42, 50, 50, 42, 50, 50, 42, 1, 1, 1, 2, 2, 1, 2, 2, 7, 7, 7, 7, 7, 7, 50, 50, 42, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 826) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350699900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350699900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000350699900 none O=C(N1CCC[C@@H]1c1n[nH]c(c2ccccc2)n1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 9, 9, 9, 9, 9, 41, 41, 41, 41, 41, 50, 50, 42, 50, 50, 41, 1, 1, 1, 2, 2, 1, 2, 2, 9, 9, 9, 9, 9, 9, 50, 50, 46, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350699900 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350699900 Building ZINC000652580815 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652580815 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/827 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/827' -> `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)N1CCC12CCCC2) `ZINC000652580815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652580815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000652580815 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 22, 22, 8, 22, 22, 5, 5, 1, 1, 1, 2, 9, 14, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 22, 22, 8, 22, 22, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 48 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/828 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/828' -> `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)N1CCC12CCCC2) `ZINC000652580815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652580815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000652580815 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 18, 5, 18, 18, 5, 5, 1, 1, 1, 2, 9, 14, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 18, 18, 5, 18, 18, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 45 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000652580815 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 Building ZINC000652580815 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652580815 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 827) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC12CCCC2) `ZINC000652580815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652580815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000652580815 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 22, 22, 8, 22, 22, 5, 5, 1, 1, 1, 2, 9, 14, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 22, 22, 8, 22, 22, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 48 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 828) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC12CCCC2) `ZINC000652580815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652580815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000652580815 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC12CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 18, 5, 18, 18, 5, 5, 1, 1, 1, 2, 9, 14, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 18, 18, 5, 18, 18, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 45 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000652580815 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000652580815 Building ZINC000350806357 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350806357 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/829 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(F)cc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350806357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350806357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000350806357 none COc1c(F)cc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 17, 17, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/830 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(F)cc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350806357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350806357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000350806357 none COc1c(F)cc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 17, 17, 9, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 17, 17, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350806357 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 Building ZINC000350806357 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350806357 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 829) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1c(F)cc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350806357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350806357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000350806357 none COc1c(F)cc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 24, 24, 24, 17, 17, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 830) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1c(F)cc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000350806357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350806357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000350806357 none COc1c(F)cc(F)cc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 17, 17, 9, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 17, 17, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350806357 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806357 Building ZINC000350806398 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350806398 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/831 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350806398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350806398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350806398 none COCC(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 6, 34, 34, 5, 6, 7, 7, 7, 7, 7, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 48, 48, 48, 48, 48, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/832 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350806398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350806398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350806398 none COCC(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 6, 33, 33, 5, 6, 7, 7, 7, 7, 7, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 48, 48, 48, 48, 48, 33, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 209 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350806398 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 Building ZINC000350806398 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350806398 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 831) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCC(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350806398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350806398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350806398 none COCC(C)(C)N(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 6, 34, 34, 5, 6, 7, 7, 7, 7, 7, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 48, 48, 48, 48, 48, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 832) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COCC(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000350806398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350806398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000350806398 none COCC(C)(C)N(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 6, 33, 33, 5, 6, 7, 7, 7, 7, 7, 7, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 48, 48, 48, 48, 48, 33, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 209 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350806398 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350806398 Building ZINC000488284966 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488284966 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/833 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C) `ZINC000488284966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488284966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000488284966 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 21, 21, 21, 50, 50, 50, 50, 21, 21, 21, 2, 2, 2, 2, 2, 2, 10, 21, 50, 50, 50, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/834 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C) `ZINC000488284966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488284966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000488284966 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 3, 3, 3, 3, 3, 3, 10, 22, 50, 50, 50, 22, 22, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488284966 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 Building ZINC000488284966 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488284966 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 833) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C) `ZINC000488284966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488284966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000488284966 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 21, 21, 21, 50, 50, 50, 50, 21, 21, 21, 2, 2, 2, 2, 2, 2, 10, 21, 50, 50, 50, 21, 21, 21] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 834) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C) `ZINC000488284966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488284966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000488284966 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(c2ccsc2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 3, 3, 3, 3, 3, 3, 10, 22, 50, 50, 50, 22, 22, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488284966 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488284966 Building ZINC000350862989 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350862989 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/835 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1) `ZINC000350862989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350862989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000350862989 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 16, 1, 16, 1, 8, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 25, 25, 11, 11, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 4, 11, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/836 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1) `ZINC000350862989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350862989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000350862989 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 16, 1, 16, 1, 8, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 10, 10, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 5, 13, 13, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350862989 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 Building ZINC000350862989 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350862989 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 835) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1) `ZINC000350862989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350862989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000350862989 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 16, 1, 16, 1, 8, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 25, 25, 11, 11, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 4, 11, 11, 11] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 836) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1) `ZINC000350862989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350862989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000350862989 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cncc(Cl)c2Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 16, 1, 16, 1, 8, 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, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 10, 10, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 5, 13, 13, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350862989 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350862989 Building ZINC000350929558 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350929558 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/837 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350929558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350929558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929558 none O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 13, 13, 13, 13, 13, 13, 13, 22, 50, 50, 50, 50, 13, 13, 1, 1, 1, 3, 3, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/838 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350929558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350929558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929558 none O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 22, 50, 50, 50, 50, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350929558 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 Building ZINC000350929558 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350929558 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 837) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350929558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350929558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929558 none O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 13, 13, 13, 13, 13, 13, 13, 22, 50, 50, 50, 50, 13, 13, 1, 1, 1, 3, 3, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 838) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350929558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350929558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929558 none O=C(N[C@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 22, 50, 50, 50, 50, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350929558 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929558 Building ZINC000350929566 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350929566 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/839 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350929566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350929566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929566 none O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 22, 49, 49, 49, 49, 13, 13, 1, 1, 1, 4, 4, 1, 4, 4, 5, 13, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/840 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350929566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350929566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929566 none O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 13, 13, 13, 13, 13, 13, 13, 24, 50, 50, 50, 50, 13, 13, 1, 1, 1, 3, 3, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350929566 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 Building ZINC000350929566 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350929566 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 839) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000350929566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350929566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929566 none O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 9, 13, 13, 13, 13, 13, 13, 13, 22, 49, 49, 49, 49, 13, 13, 1, 1, 1, 4, 4, 1, 4, 4, 5, 13, 13, 13, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 1, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 840) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000350929566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350929566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC000350929566 none O=C(N[C@@H]1CCCc2cn(C3CCCC3)nc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 13, 13, 13, 13, 13, 13, 13, 24, 50, 50, 50, 50, 13, 13, 1, 1, 1, 3, 3, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350929566 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350929566 Building ZINC000350953532 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350953532 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/841 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1) `ZINC000350953532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350953532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350953532 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 20, 20, 15, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/842 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1) `ZINC000350953532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350953532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350953532 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 20, 20, 12, 12, 49, 49, 49, 49, 49, 49, 49, 20, 20, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 49, 49, 49, 49, 49, 49, 49, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350953532 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 Building ZINC000350953532 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000350953532 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 841) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1) `ZINC000350953532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000350953532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350953532 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 20, 20, 15, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 842) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1) `ZINC000350953532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000350953532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000350953532 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccc(COc2ccccc2)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 20, 20, 12, 12, 49, 49, 49, 49, 49, 49, 49, 20, 20, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 49, 49, 49, 49, 49, 49, 49, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000350953532 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000350953532 Building ZINC000071882480 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000071882480 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/843 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl) `ZINC000071882480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000071882480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000071882480 none COc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 27, 40, 40, 34, 40, 40, 40, 3, 3, 3, 3, 2, 3, 8, 8, 8, 27, 27, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/844 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl) `ZINC000071882480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000071882480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000071882480 none COc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 3, 3, 8, 8, 27, 39, 39, 27, 39, 39, 39, 3, 3, 3, 3, 3, 3, 8, 8, 8, 27, 27, 39, 39, 33, 39] 50 rigid atoms, others: [8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000071882480 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 Building ZINC000071882480 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000071882480 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 843) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl) `ZINC000071882480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000071882480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000071882480 none COc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 27, 40, 40, 34, 40, 40, 40, 3, 3, 3, 3, 2, 3, 8, 8, 8, 27, 27, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 844) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl) `ZINC000071882480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000071882480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000071882480 none COc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 3, 3, 8, 8, 27, 39, 39, 27, 39, 39, 39, 3, 3, 3, 3, 3, 3, 8, 8, 8, 27, 27, 39, 39, 33, 39] 50 rigid atoms, others: [8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000071882480 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000071882480 Building ZINC000351183113 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351183113 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/845 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)cn1) `ZINC000351183113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351183113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351183113 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/846 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)cn1) `ZINC000351183113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351183113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351183113 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 3, 11, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 22, 22, 22, 22, 22, 22, 22, 22, 10] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351183113 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 Building ZINC000351183113 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351183113 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 845) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)cn1) `ZINC000351183113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351183113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351183113 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 20, 20, 10, 10, 1, 1, 1, 2, 9, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 18, 18, 18, 18, 18, 18, 18, 18, 10] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 846) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)cn1) `ZINC000351183113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351183113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351183113 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCc3c(F)ccc(F)c32)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.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 15, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 3, 11, 18, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 22, 22, 22, 22, 22, 22, 22, 22, 10] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351183113 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351183113 Building ZINC000488899466 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488899466 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/847 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl) `ZINC000488899466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488899466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000488899466 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 12, 1, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 25, 25, 25, 12, 12, 11, 11, 11, 11, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/848 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl) `ZINC000488899466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488899466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000488899466 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 12, 1, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 26, 26, 26, 12, 12, 11, 11, 11, 11, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488899466 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 Building ZINC000488899466 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488899466 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 847) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl) `ZINC000488899466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488899466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000488899466 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 12, 1, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 25, 25, 25, 12, 12, 11, 11, 11, 11, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 848) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl) `ZINC000488899466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488899466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000488899466 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3ccc(F)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 12, 1, 12, 12, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 26, 26, 26, 12, 12, 11, 11, 11, 11, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488899466 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488899466 Building ZINC000351271001 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271001 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/849 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/850 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/851 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/851' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/852 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/852' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271001 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 Building ZINC000351271001 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271001 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 849) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 850) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 851) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 852) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271001 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 Building ZINC000351271001 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271001 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 849) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 850) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 851) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 852) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271001 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 Building ZINC000351271001 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271001 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 849) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 850) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 851) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 852) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271001 none C[C@@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271001 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271001 Building ZINC000351271002 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271002 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/853 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/854 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/855 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/855' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/856 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/856' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271002 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 Building ZINC000351271002 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271002 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 853) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 854) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 855) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 856) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271002 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 Building ZINC000351271002 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271002 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 853) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 854) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 855) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 856) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271002 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 Building ZINC000351271002 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351271002 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 853) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 854) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 46, 46, 46, 46, 46, 47, 50, 50, 47, 50, 50, 46, 46, 46, 12, 12, 2, 3, 3, 3, 3, 3, 46, 46, 46, 46, 46, 46, 47, 47, 50, 50, 47, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 855) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 856) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1) `ZINC000351271002.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351271002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351271002 none C[C@]1(CNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCCN1Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50, 46, 46, 46, 12, 12, 3, 2, 2, 1, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 46, 50, 50] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351271002 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351271002 Building ZINC000488958188 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488958188 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/857 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488958188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958188 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 15, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/858 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488958188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958188 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488958188 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 Building ZINC000488958188 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488958188 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 857) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488958188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958188 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 15, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 858) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488958188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958188 none O=C(N[C@@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488958188 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958188 Building ZINC000488958190 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488958190 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/859 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488958190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958190 none O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 36, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 5, 5, 1, 5, 5, 5, 6, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/860 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488958190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958190 none O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 39, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488958190 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 Building ZINC000488958190 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488958190 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 859) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488958190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958190 none O=C(N[C@H]1CCCC(F)(F)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 36, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 5, 5, 1, 5, 5, 5, 6, 39, 39, 39, 39, 39, 39, 39, 39, 5, 5, 5, 5] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 860) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000488958190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488958190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000488958190 none O=C(N[C@H]1CCCC(F)(F)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 15, 15, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 10, 39, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 1, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 6, 6, 6, 6] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488958190 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488958190 Building ZINC000488988567 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488988567 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/861 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(F)c(F)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488988567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488988567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000488988567 none O=C(N1CCc2ccc(F)c(F)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/862 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(F)c(F)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488988567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488988567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000488988567 none O=C(N1CCc2ccc(F)c(F)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488988567 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 Building ZINC000488988567 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000488988567 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 861) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccc(F)c(F)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488988567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000488988567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000488988567 none O=C(N1CCc2ccc(F)c(F)c2C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 11, 11, 6, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 6, 11, 11, 11, 11, 11, 11, 11, 11] 50 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 862) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccc(F)c(F)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000488988567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000488988567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000488988567 none O=C(N1CCc2ccc(F)c(F)c2C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 15, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 6, 10, 10, 10, 10, 10, 10, 10, 10] 50 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000488988567 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000488988567 Building ZINC000351404938 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351404938 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/863 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/863' -> `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]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 11, 11, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/864 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/864' -> `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]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 11, 11, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/865 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/865' -> `2.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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 14, 14, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/866 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/866' -> `3.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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 13, 27, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351404938 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 Building ZINC000351404938 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351404938 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 863) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 11, 11, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 864) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 11, 11, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 865) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 14, 14, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 866) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 13, 27, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351404938 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 Building ZINC000351404938 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351404938 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 863) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 11, 11, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 864) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 11, 11, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 865) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 14, 14, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 866) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 13, 27, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351404938 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 Building ZINC000351404938 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351404938 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 863) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 11, 11, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 864) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 11, 11, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 865) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 11, 11, 11, 11, 24, 24, 14, 14, 24, 24, 11, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 11, 11, 24, 24, 24, 24, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 866) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2C[C@@H](c3ccc(F)cc3)C2)cn1) `ZINC000351404938.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351404938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351404938 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2C[C@@H](c3ccc(F)cc3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 13, 27, 27, 27, 11, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 2, 11, 11, 27, 27, 27, 27, 11, 11, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351404938 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351404938 Building ZINC000351456697 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351456697 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/867 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/868 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/869 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/869' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/870 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/870' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351456697 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 Building ZINC000351456697 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351456697 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 867) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 868) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 869) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 870) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351456697 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 Building ZINC000351456697 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351456697 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 867) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 868) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 869) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 870) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351456697 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 Building ZINC000351456697 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000351456697 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 867) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 868) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 14, 14, 9, 14, 14, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 18, 18, 18, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 14, 14, 5, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 869) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 870) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000351456697.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000351456697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000351456697 none CC(C)N(C)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 15, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 5, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351456697 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351456697 Building ZINC000351507764 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351507764 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/871 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351507764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507764 none O=C(N[C@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/872 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351507764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507764 none O=C(N[C@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351507764 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 Building ZINC000351507764 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351507764 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 871) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351507764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507764 none O=C(N[C@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 17, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 872) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351507764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507764 none O=C(N[C@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 5, 5] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351507764 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507764 Building ZINC000351507768 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351507768 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/873 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351507768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507768 none O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/874 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351507768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507768 none O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351507768 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 Building ZINC000351507768 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351507768 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 873) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351507768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507768 none O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 1, 2, 5, 5, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 874) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351507768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351507768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000351507768 none O=C(N[C@@H]1CCCOc2c(F)cccc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351507768 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351507768 Building ZINC000351513614 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351513614 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/875 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351513614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351513614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351513614 none O=C(NCc1ccccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 35, 35, 31, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/876 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351513614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351513614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351513614 none O=C(NCc1ccccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 35, 35, 28, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351513614 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 Building ZINC000351513614 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351513614 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 875) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351513614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351513614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351513614 none O=C(NCc1ccccc1N1CCCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 35, 35, 31, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 876) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351513614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351513614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351513614 none O=C(NCc1ccccc1N1CCCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 35, 35, 28, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 13, 13, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351513614 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351513614 Building ZINC000351533886 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351533886 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/877 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351533886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533886 none O=C(N[C@@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 16, 16, 8, 16, 16, 8, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 8, 16, 16, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/878 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351533886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533886 none O=C(N[C@@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 8, 8, 16, 16, 8, 16, 16, 8, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 8, 16, 16, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351533886 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 Building ZINC000351533886 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351533886 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 877) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351533886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533886 none O=C(N[C@@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 16, 16, 8, 16, 16, 8, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 8, 16, 16, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 878) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351533886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533886 none O=C(N[C@@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 8, 8, 16, 16, 8, 16, 16, 8, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 8, 16, 16, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351533886 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533886 Building ZINC000351533889 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351533889 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/879 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351533889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533889 none O=C(N[C@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 8, 8, 16, 16, 8, 16, 16, 8, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 8, 16, 16, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/880 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351533889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533889 none O=C(N[C@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 16, 16, 8, 16, 16, 8, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 8, 16, 16, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351533889 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 Building ZINC000351533889 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351533889 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 879) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351533889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533889 none O=C(N[C@H](c1ccccc1)C(F)F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 8, 8, 16, 16, 8, 16, 16, 8, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 5, 16, 16, 8, 16, 16, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 880) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351533889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351533889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000351533889 none O=C(N[C@H](c1ccccc1)C(F)F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 16, 16, 8, 16, 16, 8, 21, 21, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 8, 16, 16, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351533889 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351533889 Building ZINC000351555782 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351555782 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/881 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2cccc(O)c2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351555782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351555782 none O=C(Nc1nc(c2cccc(O)c2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 100, 50, 7, 3, 3, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/882 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2cccc(O)c2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351555782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351555782 none O=C(Nc1nc(c2cccc(O)c2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 100, 50, 7, 3, 3, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351555782 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 Building ZINC000351555782 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351555782 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 881) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(c2cccc(O)c2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351555782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351555782 none O=C(Nc1nc(c2cccc(O)c2)cs1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 100, 50, 7, 3, 3, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 882) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1nc(c2cccc(O)c2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351555782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351555782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351555782 none O=C(Nc1nc(c2cccc(O)c2)cs1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 7, 7, 7, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 50, 50, 50, 100, 50, 7, 3, 3, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351555782 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351555782 Building ZINC000351564400 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351564400 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/883 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351564400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351564400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351564400 none O=C(Nc1ccc(Cl)cc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 22, 22, 10, 22, 22, 22, 22, 48, 48, 48, 48, 1, 1, 1, 5, 5, 2, 5, 5, 5, 6, 22, 22, 22, 48, 48, 48, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/884 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351564400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351564400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351564400 none O=C(Nc1ccc(Cl)cc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 22, 22, 12, 22, 22, 22, 22, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 22, 22, 22, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351564400 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 Building ZINC000351564400 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351564400 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 883) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(Cl)cc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351564400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351564400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351564400 none O=C(Nc1ccc(Cl)cc1n1cccn1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 22, 22, 10, 22, 22, 22, 22, 48, 48, 48, 48, 1, 1, 1, 5, 5, 2, 5, 5, 5, 6, 22, 22, 22, 48, 48, 48, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 884) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(Cl)cc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000351564400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351564400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000351564400 none O=C(Nc1ccc(Cl)cc1n1cccn1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 15, 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, 7, 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, 22, 22, 12, 22, 22, 22, 22, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 22, 22, 22, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351564400 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351564400 Building ZINC000489433467 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489433467 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/885 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)ccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000489433467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489433467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489433467 none Cc1cc(F)ccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 28, 30, 30, 21, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 21, 21, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/886 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)ccc1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000489433467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489433467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489433467 none Cc1cc(F)ccc1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 28, 28, 20, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 20, 20, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000489433467 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 Building ZINC000489433467 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000489433467 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 885) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(F)ccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000489433467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489433467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489433467 none Cc1cc(F)ccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 28, 30, 30, 21, 6, 3, 6, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 21, 21, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 886) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc(F)ccc1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000489433467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489433467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000489433467 none Cc1cc(F)ccc1CN(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 28, 28, 20, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 20, 20, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000489433467 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000489433467 Building ZINC000351578805 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351578805 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/887 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000351578805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351578805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000351578805 none Cc1nc(CC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/888 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000351578805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351578805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000351578805 none Cc1nc(CC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351578805 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 Building ZINC000351578805 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351578805 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 887) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(CC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000351578805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351578805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000351578805 none Cc1nc(CC(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 20, 20, 20, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 888) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nc(CC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1) `ZINC000351578805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351578805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000351578805 none Cc1nc(CC(C)C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 14, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 19, 19, 19, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/318708/xbg-8058115.33/working/building/ZINC000351578805 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351578805 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351578805 Building ZINC000351582739 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351582739 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/889 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)cn1) `ZINC000351582739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351582739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000351582739 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 11, 25, 25, 11, 11, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 21, 21, 6, 21, 21, 6, 6, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 4, 21, 21, 6, 21, 21, 6, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/890 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)cn1) `ZINC000351582739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351582739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000351582739 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 24, 24, 10, 10, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 26, 26, 6, 26, 26, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 4, 26, 26, 8, 26, 26, 6, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351582739 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 Building ZINC000351582739 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351582739 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 889) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)cn1) `ZINC000351582739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351582739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000351582739 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 11, 25, 25, 11, 11, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 21, 21, 6, 21, 21, 6, 6, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 4, 21, 21, 6, 21, 21, 6, 11] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 890) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)cn1) `ZINC000351582739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351582739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000351582739 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2nc(c3ccccc3)co2)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.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 10, 24, 24, 10, 10, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 26, 26, 6, 26, 26, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 4, 26, 26, 8, 26, 26, 6, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351582739 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351582739 Building ZINC000351591664 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351591664 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/891 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(F)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351591664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351591664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000351591664 none O=C(NCC1(c2cccc(F)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 20, 29, 29, 29, 29, 29, 29, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 29, 29, 29, 29, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/892 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(F)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351591664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351591664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000351591664 none O=C(NCC1(c2cccc(F)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 23, 29, 29, 29, 29, 29, 29, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 29, 29, 29, 29, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351591664 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 Building ZINC000351591664 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351591664 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 891) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCC1(c2cccc(F)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351591664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351591664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000351591664 none O=C(NCC1(c2cccc(F)c2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 20, 29, 29, 29, 29, 29, 29, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 11, 11, 29, 29, 29, 29, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 892) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCC1(c2cccc(F)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351591664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351591664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000351591664 none O=C(NCC1(c2cccc(F)c2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 23, 29, 29, 29, 29, 29, 29, 23, 23, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 11, 11, 29, 29, 29, 29, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351591664 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351591664 Building ZINC000351629964 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351629964 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/893 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1) `ZINC000351629964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351629964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351629964 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 22, 22, 12, 12, 1, 1, 1, 1, 6, 6, 6, 8, 15, 15, 8, 8, 15, 15, 8, 8, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 6, 15, 15, 15, 15, 8, 8, 8, 8, 12] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/894 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1) `ZINC000351629964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351629964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351629964 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 1, 1, 1, 1, 6, 6, 6, 8, 19, 19, 8, 8, 19, 19, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 6, 19, 19, 19, 19, 8, 8, 8, 8, 12] 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: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351629964 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 Building ZINC000351629964 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351629964 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 893) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1) `ZINC000351629964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351629964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351629964 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 12, 22, 22, 12, 12, 1, 1, 1, 1, 6, 6, 6, 8, 15, 15, 8, 8, 15, 15, 8, 8, 12, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 6, 15, 15, 15, 15, 8, 8, 8, 8, 12] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 894) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1) `ZINC000351629964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351629964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351629964 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccc(Cl)cc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 1, 1, 1, 1, 6, 6, 6, 8, 19, 19, 8, 8, 19, 19, 8, 8, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 6, 19, 19, 19, 19, 8, 8, 8, 8, 12] 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: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351629964 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351629964 Building ZINC000351670275 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351670275 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/895 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351670275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351670275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351670275 none O=C(N1CCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10] 41 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: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/896 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351670275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351670275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351670275 none O=C(N1CCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9] 40 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: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351670275 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 Building ZINC000351670275 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351670275 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 895) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351670275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351670275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351670275 none O=C(N1CCOc2c(Cl)cccc21)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10] 41 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: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 896) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351670275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351670275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351670275 none O=C(N1CCOc2c(Cl)cccc21)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [11, 2, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9] 40 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: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351670275 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351670275 Building ZINC000351688600 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351688600 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/897 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C) `ZINC000351688600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351688600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000351688600 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 50, 15, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/898 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C) `ZINC000351688600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351688600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000351688600 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 50, 15, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351688600 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 Building ZINC000351688600 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351688600 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 897) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C) `ZINC000351688600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351688600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000351688600 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 50, 15, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 898) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C) `ZINC000351688600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351688600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000351688600 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 50, 15, 15, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 15, 15, 15, 15, 15, 50, 50, 50, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351688600 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351688600 Building ZINC000351707847 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351707847 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/899 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl) `ZINC000351707847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351707847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707847 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 30, 45, 45, 45, 43, 45, 45, 45, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 30, 30, 45, 43, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/900 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl) `ZINC000351707847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351707847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707847 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 13, 13, 13, 13, 13, 13, 23, 37, 37, 37, 23, 37, 37, 37, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 23, 23, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351707847 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 Building ZINC000351707847 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351707847 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 899) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl) `ZINC000351707847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351707847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707847 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 30, 45, 45, 45, 43, 45, 45, 45, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 30, 30, 45, 43, 45] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 900) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl) `ZINC000351707847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351707847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707847 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 13, 13, 13, 13, 13, 13, 23, 37, 37, 37, 23, 37, 37, 37, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 23, 23, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351707847 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707847 Building ZINC000351707848 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351707848 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/901 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000351707848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351707848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707848 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 10, 10, 10, 10, 10, 10, 21, 33, 33, 33, 21, 33, 33, 33, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 21, 21, 33, 33, 33] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/902 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000351707848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351707848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707848 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 13, 13, 28, 41, 41, 41, 37, 41, 41, 41, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 28, 28, 41, 39, 41] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351707848 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 Building ZINC000351707848 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351707848 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 901) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000351707848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351707848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707848 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 10, 10, 10, 10, 10, 10, 21, 33, 33, 33, 21, 33, 33, 33, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 21, 21, 33, 33, 33] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 902) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl) `ZINC000351707848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351707848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000351707848 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1Cc1c(F)cccc1Cl 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', 'H', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 13, 13, 28, 41, 41, 41, 37, 41, 41, 41, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 28, 28, 41, 39, 41] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351707848 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351707848 Building ZINC000351727031 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351727031 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/903 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1) `ZINC000351727031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351727031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351727031 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 22, 22, 18, 22, 22, 22, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/904 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1) `ZINC000351727031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351727031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351727031 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 22, 22, 18, 22, 22, 22, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351727031 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 Building ZINC000351727031 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351727031 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 903) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1) `ZINC000351727031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351727031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351727031 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 22, 22, 18, 22, 22, 22, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 904) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1) `ZINC000351727031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351727031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000351727031 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OCc1ccccc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 22, 22, 18, 22, 22, 22, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/318708/xbg-8058115.33/working/building/ZINC000351727031 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351727031 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351727031 Building ZINC000351732305 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351732305 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/905 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351732305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351732305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000351732305 none O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 14, 14, 14, 14, 14, 14, 20, 25, 35, 35, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/906 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351732305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351732305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000351732305 none O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 14, 14, 10, 14, 14, 14, 19, 25, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351732305 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 Building ZINC000351732305 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351732305 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 905) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351732305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351732305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000351732305 none O=C(NCc1ccccc1OCC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 14, 14, 14, 14, 14, 14, 20, 25, 35, 35, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 906) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000351732305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351732305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000351732305 none O=C(NCc1ccccc1OCC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 8, 14, 14, 10, 14, 14, 14, 19, 25, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 14, 14, 14, 14, 25, 25, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351732305 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351732305 Building ZINC000351783419 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351783419 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/907 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1) `ZINC000351783419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351783419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351783419 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 5, 5, 9, 9, 19, 19, 19, 19, 19, 19, 9, 9, 9, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 5, 19, 19, 19, 16, 19, 19, 19, 9, 9, 9, 9, 9, 9, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/908 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1) `ZINC000351783419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351783419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351783419 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 10, 10, 1, 1, 1, 1, 5, 5, 9, 9, 22, 22, 22, 22, 22, 22, 9, 9, 9, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 5, 22, 22, 22, 18, 22, 22, 22, 9, 9, 9, 9, 9, 9, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351783419 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 Building ZINC000351783419 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351783419 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 907) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1) `ZINC000351783419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351783419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351783419 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 21, 21, 10, 10, 1, 1, 1, 1, 5, 5, 9, 9, 19, 19, 19, 19, 19, 19, 9, 9, 9, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 5, 19, 19, 19, 16, 19, 19, 19, 9, 9, 9, 9, 9, 9, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 908) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1) `ZINC000351783419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351783419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000351783419 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(Cc3ccccc3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 10, 10, 1, 1, 1, 1, 5, 5, 9, 9, 22, 22, 22, 22, 22, 22, 9, 9, 9, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 5, 22, 22, 22, 18, 22, 22, 22, 9, 9, 9, 9, 9, 9, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351783419 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351783419 Building ZINC000351794414 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351794414 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/909 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2cccnc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000351794414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351794414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351794414 none Cc1cc2cccnc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 11, 16, 16, 16, 16, 16, 16, 16, 16, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 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, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/910 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2cccnc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000351794414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351794414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351794414 none Cc1cc2cccnc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 14, 14, 14, 14, 14, 14, 14, 14, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351794414 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 Building ZINC000351794414 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351794414 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 909) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc2cccnc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000351794414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351794414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351794414 none Cc1cc2cccnc2c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 11, 16, 16, 16, 16, 16, 16, 16, 16, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 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, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 910) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1cc2cccnc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1) `ZINC000351794414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351794414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000351794414 none Cc1cc2cccnc2c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 14, 14, 14, 14, 14, 14, 14, 14, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351794414 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351794414 Building ZINC000351942629 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351942629 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/911 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351942629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942629 none Cc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 8, 17, 17, 16, 16, 16, 16, 8, 16, 16, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/912 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351942629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942629 none Cc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 8, 16, 16, 16, 16, 16, 16, 8, 16, 16, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351942629 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 Building ZINC000351942629 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351942629 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 911) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351942629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942629 none Cc1ccccc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 8, 17, 17, 16, 16, 16, 16, 8, 16, 16, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 912) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351942629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942629 none Cc1ccccc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 8, 16, 16, 16, 16, 16, 16, 8, 16, 16, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 16, 16, 16, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351942629 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942629 Building ZINC000351942630 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351942630 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/913 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351942630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942630 none Cc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 16, 16, 16, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/914 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351942630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942630 none Cc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 19, 19, 19, 9, 8, 15, 15, 14, 14, 14, 14, 8, 14, 14, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 15, 15, 15, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351942630 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 Building ZINC000351942630 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000351942630 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 913) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000351942630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942630 none Cc1ccccc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 16, 16, 16, 16, 16] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 914) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1) `ZINC000351942630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000351942630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000351942630 none Cc1ccccc1[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 14, 14, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 19, 19, 19, 9, 8, 15, 15, 14, 14, 14, 14, 8, 14, 14, 4, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 15, 15, 15, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000351942630 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000351942630 Building ZINC000352038700 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352038700 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/915 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1) `ZINC000352038700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352038700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352038700 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 20, 20, 20, 20, 20, 20, 9, 9, 9, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/916 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1) `ZINC000352038700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352038700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352038700 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 24, 24, 24, 24, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352038700 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 Building ZINC000352038700 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352038700 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 915) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1) `ZINC000352038700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352038700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352038700 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 20, 20, 20, 20, 20, 20, 9, 9, 9, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 916) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1) `ZINC000352038700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352038700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352038700 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 24, 24, 24, 24, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352038700 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352038700 Building ZINC000352059757 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352059757 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/917 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000352059757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352059757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352059757 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 11, 45, 50, 50, 50, 11, 11, 11, 1, 1, 1, 3, 3, 1, 3, 3, 5, 11, 11, 11, 22, 3, 3, 1, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/918 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000352059757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352059757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352059757 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 10, 10, 9, 10, 46, 50, 50, 50, 10, 10, 10, 1, 1, 1, 3, 3, 1, 3, 3, 4, 10, 10, 10, 20, 3, 3, 1, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352059757 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 Building ZINC000352059757 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352059757 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 917) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000352059757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352059757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352059757 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 11, 11, 11, 11, 45, 50, 50, 50, 11, 11, 11, 1, 1, 1, 3, 3, 1, 3, 3, 5, 11, 11, 11, 22, 3, 3, 1, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 918) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000352059757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352059757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352059757 none O=C(Nc1ccc(OC(F)(F)F)cc1O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 10, 10, 9, 10, 46, 50, 50, 50, 10, 10, 10, 1, 1, 1, 3, 3, 1, 3, 3, 4, 10, 10, 10, 20, 3, 3, 1, 3, 3] 100 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352059757 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352059757 Building ZINC000352095558 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352095558 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/919 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000352095558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352095558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095558 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 34, 34, 34, 34, 34, 34, 34, 10, 34, 34, 1, 1, 1, 3, 3, 1, 3, 3, 6, 34, 34, 34, 34, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/920 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000352095558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352095558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095558 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 35, 35, 35, 35, 35, 35, 35, 10, 34, 34, 1, 1, 1, 3, 3, 1, 3, 3, 5, 35, 35, 35, 34, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352095558 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 Building ZINC000352095558 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352095558 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 919) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000352095558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352095558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095558 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 34, 34, 34, 34, 34, 34, 34, 10, 34, 34, 1, 1, 1, 3, 3, 1, 3, 3, 6, 34, 34, 34, 34, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 920) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000352095558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352095558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095558 none O=C(N[C@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 10, 10, 35, 35, 35, 35, 35, 35, 35, 10, 34, 34, 1, 1, 1, 3, 3, 1, 3, 3, 5, 35, 35, 35, 34, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352095558 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095558 Building ZINC000352095559 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352095559 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/921 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000352095559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352095559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095559 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 34, 34, 34, 34, 34, 34, 34, 9, 33, 33, 1, 1, 1, 3, 3, 1, 3, 3, 5, 34, 34, 34, 33, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/922 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000352095559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352095559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095559 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 36, 36, 36, 36, 36, 36, 36, 10, 34, 34, 1, 1, 1, 3, 3, 1, 3, 3, 6, 36, 36, 36, 34, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 170 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352095559 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 Building ZINC000352095559 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352095559 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 921) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1) `ZINC000352095559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352095559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095559 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 34, 34, 34, 34, 34, 34, 34, 9, 33, 33, 1, 1, 1, 3, 3, 1, 3, 3, 5, 34, 34, 34, 33, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 922) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000352095559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352095559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000352095559 none O=C(N[C@@H](c1cc(F)ccc1F)C(F)F)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 15, 1, 1, 1, 15, 5, 15, 15, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 10, 10, 36, 36, 36, 36, 36, 36, 36, 10, 34, 34, 1, 1, 1, 3, 3, 1, 3, 3, 6, 36, 36, 36, 34, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 170 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352095559 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352095559 Building ZINC000352116225 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352116225 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/923 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc2ccccc2o1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352116225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352116225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352116225 none O=C(NCCc1cc2ccccc2o1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 16, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 16, 16, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/924 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc2ccccc2o1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352116225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352116225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352116225 none O=C(NCCc1cc2ccccc2o1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 16, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 16, 16, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352116225 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 Building ZINC000352116225 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352116225 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 923) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCCc1cc2ccccc2o1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352116225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352116225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352116225 none O=C(NCCc1cc2ccccc2o1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 16, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 16, 16, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 924) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCCc1cc2ccccc2o1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352116225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352116225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352116225 none O=C(NCCc1cc2ccccc2o1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 16, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 16, 16, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352116225 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352116225 Building ZINC000352157993 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352157993 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/925 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/925' -> `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]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352157993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157993 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 11, 11, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 5, 17, 17, 17, 17, 17, 17, 17, 11] 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/926 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/926' -> `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]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352157993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157993 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 22, 22, 10, 10, 1, 1, 1, 1, 5, 5, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 5, 16, 16, 16, 16, 16, 16, 16, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352157993 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 Building ZINC000352157993 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352157993 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 925) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352157993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157993 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 17, 11, 11, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 5, 17, 17, 17, 17, 17, 17, 17, 11] 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 926) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352157993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157993 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 22, 22, 10, 10, 1, 1, 1, 1, 5, 5, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 5, 16, 16, 16, 16, 16, 16, 16, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352157993 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157993 Building ZINC000352157994 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352157994 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/927 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/927' -> `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]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352157994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157994 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 19, 11, 11, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 5, 17, 17, 17, 17, 17, 17, 17, 11] 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/928 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/928' -> `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]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352157994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157994 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 10, 10, 1, 1, 1, 1, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 4, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352157994 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 Building ZINC000352157994 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352157994 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 927) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352157994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157994 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 19, 19, 11, 11, 1, 1, 1, 1, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 5, 17, 17, 17, 17, 17, 17, 17, 11] 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 928) grep: /scratch/xiaobo/318708/xbg-8058115.33/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)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(Cl)ccc32)cn1) `ZINC000352157994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352157994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352157994 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(Cl)ccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 23, 10, 10, 1, 1, 1, 1, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 4, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352157994 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352157994 Building ZINC000352201093 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352201093 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/929 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352201093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201093 none CC[C@@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 5, 16, 16, 21, 21, 16, 21, 21, 2, 5, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 22, 22, 22, 22, 22, 21, 21, 21, 21, 8, 8, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/930 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352201093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201093 none CC[C@@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 4, 15, 15, 21, 21, 15, 21, 21, 2, 4, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 17, 17, 17, 17, 17, 21, 21, 21, 21, 6, 6, 6, 6, 6, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352201093 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 Building ZINC000352201093 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352201093 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 929) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352201093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201093 none CC[C@@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 5, 16, 16, 21, 21, 16, 21, 21, 2, 5, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 22, 22, 22, 22, 22, 21, 21, 21, 21, 8, 8, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 930) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352201093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201093 none CC[C@@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 4, 15, 15, 21, 21, 15, 21, 21, 2, 4, 6, 1, 2, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 17, 17, 17, 17, 17, 21, 21, 21, 21, 6, 6, 6, 6, 6, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352201093 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201093 Building ZINC000352201094 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352201094 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/931 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352201094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201094 none CC[C@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 4, 16, 16, 24, 24, 22, 24, 24, 2, 4, 6, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 19, 19, 19, 19, 19, 24, 24, 24, 24, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/932 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352201094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201094 none CC[C@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 15, 15, 20, 20, 15, 20, 20, 2, 5, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352201094 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 Building ZINC000352201094 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352201094 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 931) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352201094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201094 none CC[C@H](c1ccncc1)N(CC)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 4, 16, 16, 24, 24, 22, 24, 24, 2, 4, 6, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 19, 19, 19, 19, 19, 24, 24, 24, 24, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 932) grep: /scratch/xiaobo/318708/xbg-8058115.33/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@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352201094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352201094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000352201094 none CC[C@H](c1ccncc1)N(CC)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 15, 15, 20, 20, 15, 20, 20, 2, 5, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352201094 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352201094 Building ZINC000352220778 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352220778 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/933 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000352220778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352220778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352220778 none CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 13, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 8, 35, 35, 35, 35, 35, 17, 17, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/934 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000352220778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352220778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352220778 none CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 16, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 8, 32, 32, 32, 32, 32, 16, 16, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352220778 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 Building ZINC000352220778 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352220778 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 933) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000352220778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352220778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352220778 none CCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 13, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 8, 35, 35, 35, 35, 35, 17, 17, 8, 8, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 934) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000352220778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352220778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352220778 none CCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 16, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 8, 32, 32, 32, 32, 32, 16, 16, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352220778 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352220778 Building ZINC000352393485 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393485 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/935 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352393485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000352393485 none C[C@H](c1ccccc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 20, 20, 23, 23, 20, 23, 23, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 20, 20, 20, 23, 23, 20, 23, 23, 6, 6, 6, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/936 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](c1ccccc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352393485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000352393485 none C[C@H](c1ccccc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 20, 20, 22, 22, 20, 22, 22, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 20, 20, 20, 22, 22, 20, 22, 22, 8, 8, 8, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393485 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 Building ZINC000352393485 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393485 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 935) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccccc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352393485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000352393485 none C[C@H](c1ccccc1)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 20, 20, 23, 23, 20, 23, 23, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 20, 20, 20, 23, 23, 20, 23, 23, 6, 6, 6, 2, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 936) grep: /scratch/xiaobo/318708/xbg-8058115.33/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](c1ccccc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352393485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000352393485 none C[C@H](c1ccccc1)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 20, 20, 22, 22, 20, 22, 22, 4, 8, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 20, 20, 20, 22, 22, 20, 22, 22, 8, 8, 8, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393485 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393485 Building ZINC000352393486 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393486 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/937 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393486 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 18, 18, 18, 8, 9, 22, 22, 22, 27, 27, 22, 27, 27, 9, 9, 9, 4, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 22, 22, 22, 27, 27, 25, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/938 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393486 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 9, 10, 20, 20, 20, 25, 25, 20, 25, 25, 10, 10, 10, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 20, 20, 20, 25, 25, 20, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393486 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 Building ZINC000352393486 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393486 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 937) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393486 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 18, 18, 18, 8, 9, 22, 22, 22, 27, 27, 22, 27, 27, 9, 9, 9, 4, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 22, 22, 22, 27, 27, 25, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 938) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393486 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 9, 10, 20, 20, 20, 25, 25, 20, 25, 25, 10, 10, 10, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 20, 20, 20, 25, 25, 20, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393486 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393486 Building ZINC000352393487 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393487 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/939 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1) `ZINC000352393487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393487 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 10, 21, 21, 21, 26, 26, 26, 26, 26, 10, 10, 10, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 21, 21, 21, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/940 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1) `ZINC000352393487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393487 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 18, 18, 18, 8, 9, 23, 23, 23, 29, 29, 23, 29, 29, 9, 9, 9, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 23, 23, 23, 29, 29, 23, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393487 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 Building ZINC000352393487 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393487 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 939) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1) `ZINC000352393487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393487 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 9, 10, 21, 21, 21, 26, 26, 26, 26, 26, 10, 10, 10, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 21, 21, 21, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 940) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1) `ZINC000352393487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393487 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 18, 18, 18, 8, 9, 23, 23, 23, 29, 29, 23, 29, 29, 9, 9, 9, 3, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 23, 23, 23, 29, 29, 23, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393487 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393487 Building ZINC000352393488 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393488 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/941 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393488 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 8, 20, 18, 20, 22, 22, 20, 22, 22, 8, 8, 8, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 20, 20, 20, 22, 22, 20, 22, 22] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/942 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393488 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 6, 20, 19, 20, 22, 22, 20, 22, 22, 6, 6, 6, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 20, 20, 20, 22, 22, 20, 22, 22] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393488 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 Building ZINC000352393488 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352393488 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 941) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352393488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393488 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 8, 20, 18, 20, 22, 22, 20, 22, 22, 8, 8, 8, 4, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 20, 20, 20, 22, 22, 20, 22, 22] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 942) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1) `ZINC000352393488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352393488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000352393488 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 6, 20, 19, 20, 22, 22, 20, 22, 22, 6, 6, 6, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 20, 20, 20, 22, 22, 20, 22, 22] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352393488 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352393488 Building ZINC000352420133 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352420133 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/943 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352420133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420133 none Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 8, 16, 8, 1, 8, 1, 1, 1, 5, 5, 2, 5, 5, 5, 16, 24, 24, 24, 29, 29, 29, 29, 29, 29, 8, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 156 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/944 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352420133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420133 none Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 8, 15, 8, 1, 8, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 23, 23, 23, 27, 27, 27, 27, 27, 27, 8, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 27] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352420133 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 Building ZINC000352420133 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352420133 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 943) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352420133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420133 none Cn1cc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 8, 16, 8, 1, 8, 1, 1, 1, 5, 5, 2, 5, 5, 5, 16, 24, 24, 24, 29, 29, 29, 29, 29, 29, 8, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 29] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 156 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 944) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352420133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420133 none Cn1cc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 8, 15, 8, 1, 8, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 23, 23, 23, 27, 27, 27, 27, 27, 27, 8, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 27] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352420133 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420133 Building ZINC000352420134 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352420134 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/945 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352420134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420134 none Cn1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 15, 8, 15, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 15, 24, 24, 24, 26, 26, 26, 26, 26, 26, 8, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 26] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/946 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352420134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420134 none Cn1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 15, 8, 15, 8, 1, 8, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 24, 24, 24, 28, 28, 28, 28, 28, 28, 8, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 28] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352420134 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 Building ZINC000352420134 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352420134 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 945) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352420134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420134 none Cn1cc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 15, 8, 15, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 15, 24, 24, 24, 26, 26, 26, 26, 26, 26, 8, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 26] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 946) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cn1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1) `ZINC000352420134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352420134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000352420134 none Cn1cc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 15, 8, 15, 8, 1, 8, 1, 1, 1, 5, 5, 1, 1, 5, 5, 15, 24, 24, 24, 28, 28, 28, 28, 28, 28, 8, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 28] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352420134 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352420134 Building ZINC000352451323 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352451323 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/947 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352451323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352451323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000352451323 none O=C(N1CCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 17 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/948 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352451323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352451323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000352451323 none O=C(N1CCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5] 16 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352451323 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 Building ZINC000352451323 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352451323 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 947) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352451323.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352451323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000352451323 none O=C(N1CCc2ccc(Br)cc21)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 17 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 948) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352451323.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352451323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000352451323 none O=C(N1CCc2ccc(Br)cc21)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5] 16 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352451323 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352451323 Building ZINC000352580208 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352580208 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/949 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1) `ZINC000352580208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352580208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352580208 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 27, 13, 13, 36, 36, 36, 27, 27, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 27, 27, 36, 36, 36, 27, 27, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/950 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1) `ZINC000352580208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352580208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352580208 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 13, 14, 34, 34, 34, 24, 24, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 24, 24, 34, 34, 34, 24, 24, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352580208 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 Building ZINC000352580208 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352580208 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 949) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1) `ZINC000352580208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352580208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352580208 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 27, 27, 13, 13, 36, 36, 36, 27, 27, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 27, 27, 36, 36, 36, 27, 27, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 950) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1) `ZINC000352580208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352580208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000352580208 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(C(C)(F)F)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 13, 14, 34, 34, 34, 24, 24, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 13, 13, 24, 24, 34, 34, 34, 24, 24, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352580208 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352580208 Building ZINC000490622555 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490622555 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/951 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1) `ZINC000490622555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490622555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000490622555 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 4, 11, 11, 3, 3, 1, 1, 1, 1, 4, 4, 7, 10, 26, 26, 26, 26, 26, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/952 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1) `ZINC000490622555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490622555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000490622555 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 8, 10, 28, 28, 28, 28, 28, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000490622555 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 Building ZINC000490622555 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490622555 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 951) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1) `ZINC000490622555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490622555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000490622555 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 4, 11, 11, 3, 3, 1, 1, 1, 1, 4, 4, 7, 10, 26, 26, 26, 26, 26, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 99 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 952) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1) `ZINC000490622555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490622555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000490622555 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C1(C)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 8, 10, 28, 28, 28, 28, 28, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000490622555 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490622555 Building ZINC000352602872 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352602872 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/953 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCSc1ccccn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352602872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352602872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000352602872 none O=C(NCCCSc1ccccn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 14, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 10, 12, 28, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 12, 12, 12, 12, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/954 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCSc1ccccn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352602872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352602872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000352602872 none O=C(NCCCSc1ccccn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 14, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 10, 12, 26, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 12, 12, 12, 12, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352602872 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 Building ZINC000352602872 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352602872 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 953) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCCCSc1ccccn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352602872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352602872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000352602872 none O=C(NCCCSc1ccccn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 14, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 10, 12, 28, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 12, 12, 12, 12, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 954) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCCCSc1ccccn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000352602872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352602872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000352602872 none O=C(NCCCSc1ccccn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 14, 1, 1, 1, 1, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 10, 12, 26, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 12, 12, 12, 12, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352602872 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352602872 Building ZINC000352615483 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352615483 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/955 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000352615483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352615483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000352615483 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 4, 16, 16, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/956 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000352615483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352615483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000352615483 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352615483 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 Building ZINC000352615483 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352615483 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 955) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000352615483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352615483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000352615483 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 4, 16, 16, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 956) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)cc1) `ZINC000352615483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352615483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000352615483 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nc3ccccc3n2C2CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 4, 14, 14, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352615483 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352615483 Building ZINC000352616424 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352616424 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/957 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352616424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352616424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000352616424 none O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 14, 14, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/958 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352616424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352616424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000352616424 none O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 15, 15, 40, 40, 40, 40, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352616424 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 Building ZINC000352616424 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352616424 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 957) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352616424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352616424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000352616424 none O=C(NCc1nc2ccccc2n1C1CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 41, 41, 41, 41, 41, 41, 41, 41, 41, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 14, 14, 41, 41, 41, 41, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 958) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352616424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352616424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000352616424 none O=C(NCc1nc2ccccc2n1C1CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 15, 15, 40, 40, 40, 40, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352616424 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352616424 Building ZINC000490681757 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490681757 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/959 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)F)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000490681757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490681757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000490681757 none O=C(N(CC(F)F)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 13, 24, 24, 7, 17, 17, 10, 15, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 24, 17, 17, 17, 17, 3, 3, 3, 3] 27 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]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/960 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC(F)F)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000490681757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490681757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000490681757 none O=C(N(CC(F)F)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 13, 24, 24, 7, 17, 17, 10, 13, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 24, 17, 17, 17, 17, 3, 3, 3, 3] 27 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]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000490681757 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 Building ZINC000490681757 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000490681757 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 959) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N(CC(F)F)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000490681757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000490681757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000490681757 none O=C(N(CC(F)F)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 13, 24, 24, 7, 17, 17, 10, 15, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 24, 17, 17, 17, 17, 3, 3, 3, 3] 27 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]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 960) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N(CC(F)F)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000490681757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000490681757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000490681757 none O=C(N(CC(F)F)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 13, 24, 24, 7, 17, 17, 10, 13, 17, 17, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 24, 17, 17, 17, 17, 3, 3, 3, 3] 27 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]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000490681757 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000490681757 Building ZINC000352663176 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352663176 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/961 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352663176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352663176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000352663176 none CN(CCc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 18, 19, 27, 27, 19, 19, 27, 27, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 7, 7, 7, 18, 18, 19, 19, 27, 27, 27, 27, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/962 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352663176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352663176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000352663176 none CN(CCc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 18, 19, 27, 27, 19, 20, 27, 27, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 7, 7, 7, 18, 18, 19, 19, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352663176 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 Building ZINC000352663176 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352663176 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 961) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(CCc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352663176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352663176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000352663176 none CN(CCc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 18, 19, 27, 27, 19, 19, 27, 27, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 7, 7, 7, 18, 18, 19, 19, 27, 27, 27, 27, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 962) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CN(CCc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352663176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352663176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000352663176 none CN(CCc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 18, 19, 27, 27, 19, 20, 27, 27, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 7, 7, 7, 18, 18, 19, 19, 27, 27, 27, 27, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352663176 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352663176 Building ZINC000352803402 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352803402 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/963 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352803402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352803402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352803402 none CC(C)Oc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/964 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Oc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352803402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352803402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352803402 none CC(C)Oc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 32, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352803402 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 Building ZINC000352803402 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352803402 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 963) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)Oc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352803402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352803402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352803402 none CC(C)Oc1cc(F)ccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 4, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 2, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 964) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC(C)Oc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352803402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352803402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000352803402 none CC(C)Oc1cc(F)ccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 32, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352803402 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352803402 Building ZINC000352821153 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352821153 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/965 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352821153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352821153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352821153 none CSCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 8, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 29, 29, 29, 24, 24, 8, 4, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/966 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352821153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352821153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352821153 none CSCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 8, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 28, 28, 28, 24, 24, 8, 2, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352821153 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 Building ZINC000352821153 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352821153 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 965) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352821153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352821153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352821153 none CSCc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 8, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 29, 29, 29, 24, 24, 8, 4, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 966) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000352821153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352821153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352821153 none CSCc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 8, 8, 8, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 28, 28, 28, 24, 24, 8, 2, 8, 8, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352821153 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352821153 Building ZINC000579717884 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000579717884 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/967 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000579717884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000579717884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000579717884 none O=C(N1CCC(F)(c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/968 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000579717884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000579717884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000579717884 none O=C(N1CCC(F)(c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 15, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000579717884 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 Building ZINC000579717884 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000579717884 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 967) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC(F)(c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000579717884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000579717884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000579717884 none O=C(N1CCC(F)(c2ccccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 968) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: O=C(N1CCC(F)(c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000579717884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000579717884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000579717884 none O=C(N1CCC(F)(c2ccccn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 15, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 3, 3] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000579717884 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000579717884 Building ZINC000352871274 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352871274 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/969 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352871274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871274 none COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 23, 23, 23, 23, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 26, 26, 26, 23, 23, 23, 15, 15, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/970 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352871274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871274 none COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 24, 24, 24, 24, 18, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 24, 26, 26, 26, 24, 24, 24, 18, 18, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352871274 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 Building ZINC000352871274 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352871274 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 969) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352871274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871274 none COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 23, 23, 23, 23, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 26, 26, 26, 23, 23, 23, 15, 15, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 970) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352871274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871274 none COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 24, 24, 24, 24, 18, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 24, 26, 26, 26, 24, 24, 24, 18, 18, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352871274 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871274 Building ZINC000352871275 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352871275 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/971 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352871275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871275 none COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 24, 24, 24, 24, 18, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 24, 26, 26, 26, 24, 24, 24, 18, 18, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/972 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352871275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871275 none COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 23, 23, 23, 23, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 26, 26, 26, 23, 23, 23, 15, 15, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352871275 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 Building ZINC000352871275 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352871275 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 971) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352871275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871275 none COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 24, 24, 24, 24, 18, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 24, 26, 26, 26, 24, 24, 24, 18, 18, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 972) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000352871275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352871275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352871275 none COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 23, 23, 23, 23, 15, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 26, 26, 26, 23, 23, 23, 15, 15, 7, 7, 7, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352871275 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352871275 Building ZINC000352874006 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352874006 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/973 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352874006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874006 none COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 31, 13, 3, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 50, 50, 50, 49, 49, 49, 31, 31, 13, 13, 13, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/974 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352874006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874006 none COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 45, 45, 29, 11, 3, 11, 11, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 50, 50, 50, 45, 45, 45, 29, 29, 11, 11, 11, 3, 3, 3, 3, 3, 45] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352874006 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 Building ZINC000352874006 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352874006 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 973) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352874006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874006 none COc1cccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 31, 13, 3, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 49, 50, 50, 50, 49, 49, 49, 31, 31, 13, 13, 13, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 974) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352874006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874006 none COc1cccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 45, 45, 29, 11, 3, 11, 11, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 50, 50, 50, 45, 45, 45, 29, 29, 11, 11, 11, 3, 3, 3, 3, 3, 45] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352874006 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874006 Building ZINC000352874007 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352874007 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/975 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352874007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874007 none COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 45, 45, 28, 11, 3, 11, 11, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 50, 50, 50, 45, 45, 45, 28, 28, 11, 11, 11, 3, 3, 3, 3, 3, 45] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/976 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352874007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874007 none COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 31, 13, 3, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 49, 49, 49, 31, 31, 13, 13, 13, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352874007 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 Building ZINC000352874007 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352874007 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 975) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352874007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874007 none COc1cccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 45, 45, 28, 11, 3, 11, 11, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 50, 50, 50, 45, 45, 45, 28, 28, 11, 11, 11, 3, 3, 3, 3, 3, 45] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 976) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1) `ZINC000352874007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352874007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000352874007 none COc1cccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 31, 13, 3, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 50, 50, 50, 49, 49, 49, 31, 31, 13, 13, 13, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352874007 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874007 Building ZINC000352874709 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352874709 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/977 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1) `ZINC000352874709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352874709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352874709 none CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 7, 15, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 50, 50, 50, 50, 50, 46, 46, 15, 15, 7, 7, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/978 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1) `ZINC000352874709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352874709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352874709 none CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 7, 15, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 50, 50, 50, 50, 50, 46, 46, 15, 15, 7, 7, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352874709 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 Building ZINC000352874709 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352874709 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 977) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1) `ZINC000352874709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352874709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352874709 none CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 7, 15, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 50, 50, 50, 50, 50, 46, 46, 15, 15, 7, 7, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 978) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1) `ZINC000352874709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352874709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000352874709 none CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 7, 15, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 15, 50, 50, 50, 50, 50, 46, 46, 15, 15, 7, 7, 2, 2, 2, 2, 2, 15, 15, 15, 15] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352874709 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352874709 Building ZINC000352885969 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352885969 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/979 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c2ccccc2oc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352885969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352885969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000352885969 none COc1c2ccccc2oc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 48, 48, 48, 48, 12, 12, 3, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/980 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c2ccccc2oc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352885969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352885969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000352885969 none COc1c2ccccc2oc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 48, 48, 48, 48, 12, 12, 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, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352885969 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 Building ZINC000352885969 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000352885969 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 979) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1c2ccccc2oc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352885969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000352885969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000352885969 none COc1c2ccccc2oc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 48, 48, 48, 48, 12, 12, 3, 2, 2, 2, 2] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 980) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1c2ccccc2oc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000352885969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000352885969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000352885969 none COc1c2ccccc2oc1CNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 48, 48, 48, 48, 12, 12, 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, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000352885969 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000352885969 Building ZINC000077329551 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000077329551 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/981 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000077329551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329551 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/982 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000077329551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329551 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000077329551 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 Building ZINC000077329551 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000077329551 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 981) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000077329551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329551 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 982) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000077329551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329551 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000077329551 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329551 Building ZINC000077329553 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000077329553 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/983 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000077329553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329553 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/984 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000077329553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329553 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000077329553 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 Building ZINC000077329553 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000077329553 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 983) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000077329553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329553 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 984) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1) `ZINC000077329553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000077329553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000077329553 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc3c(c2)OCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000077329553 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000077329553 Building ZINC000353089990 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353089990 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/985 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000353089990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353089990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000353089990 none CSc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 16, 16, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 16, 16, 22, 22, 22, 16, 16, 4, 4, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/986 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000353089990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353089990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000353089990 none CSc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 10, 17, 17, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 17, 17, 31, 31, 31, 17, 17, 4, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353089990 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 Building ZINC000353089990 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353089990 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 985) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000353089990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353089990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000353089990 none CSc1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 16, 16, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 16, 16, 22, 22, 22, 16, 16, 4, 4, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 986) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CSc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1) `ZINC000353089990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353089990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000353089990 none CSc1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 10, 17, 17, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 17, 17, 31, 31, 31, 17, 17, 4, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353089990 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353089990 Building ZINC000353288030 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000353288030 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/987 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/988 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/989 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/989' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/990 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/990' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353288030 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 Building ZINC000353288030 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000353288030 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 987) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 988) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 989) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 990) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353288030 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 Building ZINC000353288030 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000353288030 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 987) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 988) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 989) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 990) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353288030 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 Building ZINC000353288030 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000353288030 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 987) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 988) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `2' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 2 (index: 989) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 8, 16, 18, 18, 18, 18, 18, 50, 50, 18, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `3' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 3 (index: 990) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3ccccc3F)CC2)cc1) `ZINC000353288030.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000353288030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000353288030 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(c3ccccc3F)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 14, 16, 16, 16, 16, 16, 50, 50, 22, 50, 50, 50, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353288030 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/0.* 2: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/2.* 3: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/3.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353288030 Building ZINC000353291008 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353291008 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/991 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCC1) `ZINC000353291008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353291008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000353291008 none COc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 50, 50, 50, 50, 50, 40, 20, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 14, 14, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/992 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCC1) `ZINC000353291008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353291008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000353291008 none COc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 50, 50, 50, 50, 50, 38, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353291008 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 Building ZINC000353291008 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353291008 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 991) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCC1) `ZINC000353291008.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353291008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000353291008 none COc1ccccc1C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 50, 50, 50, 50, 50, 40, 20, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 14, 14, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 992) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: COc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCC1) `ZINC000353291008.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353291008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000353291008 none COc1ccccc1C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 50, 50, 50, 50, 50, 38, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 2, 3, 3, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/318708/xbg-8058115.33/working/building/ZINC000353291008 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353291008 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353291008 Building ZINC000580105616 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000580105616 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/993 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1) `ZINC000580105616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000580105616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000580105616 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 6, 15, 15, 15, 15, 15, 15, 32, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 32, 50, 50, 50, 50, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/994 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1) `ZINC000580105616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000580105616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000580105616 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 30, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 30, 50, 50, 50, 50, 13, 13, 13, 13, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000580105616 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 Building ZINC000580105616 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000580105616 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 993) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1) `ZINC000580105616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000580105616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000580105616 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 6, 15, 15, 15, 15, 15, 15, 32, 50, 50, 50, 50, 50, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 32, 50, 50, 50, 50, 15, 15, 15, 15, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 994) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1) `ZINC000580105616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000580105616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000580105616 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@H](Nc3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 30, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 30, 50, 50, 50, 50, 13, 13, 13, 13, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 144 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000580105616 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000580105616 Building ZINC000353358538 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353358538 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/995 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353358538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358538 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 16, 16, 16, 16, 37, 16, 16, 41, 16, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 16, 16, 37, 37, 37, 41, 41, 41, 16] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/996 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353358538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358538 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 18, 18, 18, 18, 39, 18, 18, 43, 18, 10, 10, 10, 10, 10, 4, 3, 3, 3, 3, 18, 18, 39, 39, 39, 43, 43, 43, 18] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353358538 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 Building ZINC000353358538 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353358538 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 995) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353358538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358538 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 16, 16, 16, 16, 37, 16, 16, 41, 16, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 16, 16, 37, 37, 37, 41, 41, 41, 16] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 996) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353358538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358538 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 18, 18, 18, 18, 39, 18, 18, 43, 18, 10, 10, 10, 10, 10, 4, 3, 3, 3, 3, 18, 18, 39, 39, 39, 43, 43, 43, 18] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353358538 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358538 Building ZINC000353358539 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353358539 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/997 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353358539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358539 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 19, 19, 19, 19, 40, 19, 19, 44, 19, 10, 10, 10, 10, 10, 4, 3, 3, 3, 3, 19, 19, 40, 40, 40, 44, 44, 44, 19] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/998 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353358539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358539 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 16, 16, 16, 16, 37, 16, 16, 41, 16, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 16, 16, 37, 37, 37, 41, 41, 41, 16] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353358539 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 Building ZINC000353358539 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353358539 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 997) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353358539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358539 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 19, 19, 19, 19, 40, 19, 19, 44, 19, 10, 10, 10, 10, 10, 4, 3, 3, 3, 3, 19, 19, 40, 40, 40, 44, 44, 44, 19] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 998) grep: /scratch/xiaobo/318708/xbg-8058115.33/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: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1) `ZINC000353358539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353358539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000353358539 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 16, 16, 16, 16, 37, 16, 16, 41, 16, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 16, 16, 37, 37, 37, 41, 41, 41, 16] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353358539 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353358539 Building ZINC000353361166 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353361166 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/999 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000353361166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353361166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000353361166 none O=C(NCc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 47, 47, 47, 21, 47, 47, 47, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 21, 21, 47, 47, 47, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/318708/xbg-8058115.33/working/3D/1000 `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000353361166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353361166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000353361166 none O=C(NCc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 48, 48, 48, 33, 48, 48, 48, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 21, 21, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353361166 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 Building ZINC000353361166 mkdir: created directory `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353361166 mkdir: created directory `0' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/0 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 0 (index: 999) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000353361166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353361166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000353361166 none O=C(NCc1c(F)cccc1N1CCCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 47, 47, 47, 21, 47, 47, 47, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 2, 5, 5, 5, 21, 21, 47, 47, 47, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 mkdir: created directory `1' /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/1 /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Protomer 1 (index: 1000) grep: /scratch/xiaobo/318708/xbg-8058115.33/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000353361166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353361166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000353361166 none O=C(NCc1c(F)cccc1N1CCCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 21, 48, 48, 48, 33, 48, 48, 48, 50, 50, 50, 50, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 21, 21, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Finished preparing ZINC000353361166 Recording results /scratch/xiaobo/318708/xbg-8058115.33/working /scratch/xiaobo/318708/xbg-8058115.33 Appending to /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.* 0: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/0.* 1: /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166/1.* Removing working files in /scratch/xiaobo/318708/xbg-8058115.33/working/building/ZINC000353361166 /scratch/xiaobo/318708/xbg-8058115.33 Compressing combined databse files /scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/318708/xbg-8058115.33/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/318708/xbg-8058115.33/working/3D/1001' removed directory: `/scratch/xiaobo/318708/xbg-8058115.33/working/3D' rmdir: removing directory, `/scratch/xiaobo/318708/xbg-8058115.33/working/building' rmdir: removing directory, `/scratch/xiaobo/318708/xbg-8058115.33/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/318708/xbg-8058115.33' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbg' `/scratch/xiaobo/318708/xbg-8058115.33/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbg/finished' `/scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbg/finished/xbg.db2.gz' removed `/scratch/xiaobo/318708/xbg-8058115.33/finished/xbg.db2.gz' removed directory: `/scratch/xiaobo/318708/xbg-8058115.33/finished' removed directory: `/scratch/xiaobo/318708/xbg-8058115.33'